texshade 1.19 (9mar09)

git-svn-id: svn://tug.org/texlive/trunk@12351 c570f23f-e606-0410-a88d-b1316a301751

6 files changed, 2533 insertions, 1012 deletions

diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index bb80eed3bd1..a766b4725a2 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -1,4 +1,4 @@
-    TeXshade v1.18
+    TeXshade v1.19
     >>
     >> A LaTeX package for setting nucleotide and peptide alignments.
     >>
@@ -26,7 +26,7 @@
     >> ding modes.  TeXshade  combines  highest  flexibility  and the
     >> habitual TeX output quality--with reasonable time expenditure.
     >>
-    Copyright (C)  1999 - 2008  Eric Beitz
+    Copyright (C)  1999 - 2009  Eric Beitz
 
 
 
@@ -51,9 +51,12 @@
     texshade.def   Standard definitions
     AQPDNA.MSF     Example nucleotide alignment file (MSF-format)
     AQPpro.MSF     Example protein alignment file (MSF-format)
+    AQP_TC.asc     Example T-Coffee shading file
     AQP2spec.ALN   Example protein alignment file (ALN-format)
     AQP1.top       Example topology data file generated from PHD
     AQP1.phd       Example PHD secondary structure file
+    AQP1_HMM.sgl   Example HMMTOP topology data (single line format)
+    AQP1_HMM.ext   Example HMMTOP topology data (extended format)
     Standard.cod   Standard genetic code definitions
     Ciliate.cod    Ciliate macronuclear genetic code definitions
 
@@ -125,7 +128,7 @@
 3 - CONTACT
 
     E-Mail:  ebeitz@pharmazie.uni-kiel.de
-    WWW:     http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html
+    WWW:     http://www.pharmazie.uni-kiel.de/chem/
              (On-line documentation and updates)
     Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
              Gutenbergstrasse 76, D-24118 Kiel (Germany)
diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
index 1b47c480cdc..012391e2322 100644
--- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index 61e88ddf8d0..3fe76ed81cf 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -7,10 +7,10 @@
 % first run the file `texshade.ins' through LaTeX. This produces 
 % the needed style  file  `texshade.sty'  and the parameter file
 % `texshade.def' as well as several example files.  See the file
-% `texshade.txt' for further information!
+% `README' for further information!
 % 
 %
-% Copyright (C) 1999-2008 Eric Beitz
+% Copyright (C) 1999-2009 Eric Beitz
 % See the file texshade.txt
 % 
 %    \fi
@@ -308,12 +308,10 @@
 %
 %
 %    \changes{1.18}{2008-04-15}{%
-%      Corrections:  bug fixes concerning:
-%                        featurenames, ordering, numbering, setends.
-%      Introduction: T-Coffee shading can be imported and displayed 
-%                    in the alignment, in the consensus, 
-%                    in feature color scales and bar graphs by 
-%                    `shadingmode[ASCII-file]{T-Coffee}' and
+%      Corrections:  bug fixes (featurenames, ordering, numbering).
+%      Introduction: T-Coffee shading in alignment, consensus and
+%                    feature color scales and bar graphs
+%                    `shadingmode[ASCII-file]{T-Coffee}'
 %                    `includeTCoffee';
 %                    two more feature lines on top and at bottom:
 %                    `ttttop', `tttop', `bbbottom', and `bbbbottom';
@@ -321,6 +319,22 @@
 %                    via optional parameters.
 %                    }
 %
+%    \changes{1.19}{2009-03-09}{%
+%      Corrections:  horizontal scaling of logo characters with `charstretch';
+%                    further bug fixes.
+%      Introduction: selection of residues depending on PDB file coordinates;
+%                    works with `feature', `shaderegion', `shadeblock',
+%                    `tintregion', `tintblock', `emphregion',
+%                    `emphblock', `frameblock';
+%                    3D selection possible around a point, along a line, or 
+%                    within a plane;
+%                    list of selected residues printable with `printPDBlist',
+%                    or viewable during the TeX run with `messagePDBlist';
+%                    show only selected residues in alignment with `setdomain',
+%                    `domaingaprule' sets thickness of a domain separator rule,
+%                    `domaingapcolors' sets fg/bg colors for the separator rule,
+%                    these commands replace the unstable `hideblock' command.
+%                    }
 %
 %
 %
@@ -361,7 +375,7 @@
 %            for further information, updates and on-line documentation 
 %            see my homepage at
 %            \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-%    \date{v1.18; 2008/04/15\\}
+%    \date{\small v1.19; 2009/03/09\\[2pt] {*** incredible 10 years since first release ***}}
 %    \maketitle
 %    \begin{abstract}
 %      Setting alignments of nucleotides and peptides for publication 
@@ -440,6 +454,29 @@
 %    
 %    \subsection{Version History}
 %
+%    \textbf{v1.19 2009/03/09}
+%    \medskip
+%
+%    \emph{Correction:} logo characters are now horizontally 
+%    scalable using |\charstretch|. Minor bugs were fixed.
+%    
+%    \emph{Introduction:}
+%    (a) Selection of residue positions was enhanced (\ref{Lshaderegion}) 
+%    \TeXshade{} can
+%    now select residues based on their 3D coordinates provided in a 
+%    PDB structure file. 3D selection can be due to a certain distance 
+%    around a point, along a line, or above and below a plane. It
+%    works with |\feature|, |\shaderegion|, |\shadeblock|, |\tintregion|,
+%    |\tintblock|, |\emphregion|, |\emphblock|, |\frameblock|.
+%    (b) The list of selected residues is printable with |\printPDBlist| or 
+%    viewable during the \TeX{} run with |\messagePDBlist|.
+%    (c) |\hideblock| and related commands were replaced by |\setdomain|
+%    (\ref{Lsetdomain}). 
+%    This command will display only selected residues in the alignment.
+%    Thickness and colors of a domain separator rule can be set using
+%    |\domaingaprule| and |\domaingapcolors|.
+%    \bigskip
+%
 %    \textbf{v1.18 2008/04/15}
 %    \medskip
 %
@@ -458,8 +495,6 @@
 %    end definitions of the sequence section to be displayed.
 %    \bigskip
 %
-%    \newpage
-%
 %    \textbf{v1.17 2007/06/19}
 %    \medskip
 %    
@@ -482,7 +517,7 @@
 %    \bigskip
 %
 %
-%    \textbf{v1.17 2007/06/19}
+%    \textbf{v1.16 2007/02/18}
 %    \medskip
 %    
 %    \emph{Correction:} \TeXshade{} crashed when calculating conservation
@@ -547,6 +582,8 @@
 %    implemented, i.e. subfamily logos (p.\pageref{Lshowsubfamilylogo}) [14].
 %    \bigskip
 %
+%    \newpage
+%
 %    \textbf{v1.12 2005/09/20}
 %    \medskip
 %    
@@ -598,6 +635,8 @@
 %    bar graphs and color scales.
 %    \bigskip
 %    
+%    \newpage
+%
 %    \textbf{v1.9 2005/02/08}
 %    \medskip
 %    
@@ -652,6 +691,8 @@
 %    A new feature label style |helix| has been introduced.
 %    \bigskip
 %
+%    \newpage
+%
 %    \textbf{v1.6 2002/03/26}
 %    \medskip
 %    
@@ -764,6 +805,8 @@
 %    `|\Alphacount|'. All commands are described in \ref{structure}.
 %    \bigskip
 %        
+%    \newpage
+%
 %    \textbf{v1.1 1999/5/26}
 %    \medskip
 %    
@@ -1020,6 +1063,57 @@
 %    \end{verbatim}  
 %    }  
 %    
+%    Quite uncommon for an alignment shading software is the possibility
+%    to display selected residues only, e.\,g.\ to eliminate uninteresting
+%    positions from the output:
+%    \medskip
+%    
+%    \begin{texshade}{AQPpro.MSF}
+%       \setdomain{1}{80..90,100..110,120..130}
+%       \showruler{1}{top}
+%       \hidenumbering
+%       \hideconsensus
+%    \end{texshade}
+%
+%    Code:\medskip
+%
+%    \vbox{%
+%    \begin{verbatim}    
+%    \begin{texshade}{AQPpro.MSF}
+%       \setdomain{1}{80..90,100..110,120..130}
+%       \showruler{1}{top}
+%       \hidenumbering
+%       \hideconsensus
+%    \end{texshade}
+%    \end{verbatim}  
+%    }  
+%    
+%    This goes even furher. You can have \TeXshade{} select positions
+%    based on the 3D coordinates provided by a PDB file, e.\,g.\ show
+%    all residues that are within an 8 \AA{} radius around the
+%    $\alpha$-carbon of the residue at position 81:
+%    \bigskip
+%    
+%    \begin{texshade}{AQPpro.MSF}
+%       \setdomain{1}{75..86,103..103,148..148,151..153,155..156,193..195,218..219,222..222}
+%       \showruler{1}{top} \rulersteps{1}
+%       \hidenumbering
+%       \hideconsensus
+%    \end{texshade}
+%
+%    Code:\medskip
+%
+%    \vbox{%
+%    \begin{verbatim}    
+%    \begin{texshade}{AQPpro.MSF}
+%       \setdomain{1}{point[8]:1J4N.pdb,81[CA]}
+%       \showruler{1}{top} \rulersteps{1}
+%       \hidenumbering
+%       \hideconsensus
+%    \end{texshade}
+%    \end{verbatim}  
+%    }  
+%    
 %    If you like, positions where conservation is very high (here $\ge$ 80\%) can
 %    be shaded in a special color and the consensus can be shown with
 %    or without shading according to the degree of conservation:
@@ -1117,7 +1211,6 @@
 %    \begin{texshade}{AQPpro.MSF}
 %       \shadingmode[AQP_TC.asc]{T-Coffee}
 %       \setends{1}{30..63}
-%       \hideconsensus
 %       \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
 %       \showfeaturestylename{top}{feat-cons}
 %       \showconsensus{bottom}
@@ -1130,7 +1223,6 @@
 %    \begin{texshade}{AQPpro.MSF}
 %       \shadingmode[AQP_TC.asc]{T-Coffee}
 %       \setends{1}{30..63}
-%       \hideconsensus
 %       \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
 %       \showfeaturestylename{top}{feat-cons}
 %       \showconsensus{bottom}
@@ -1157,7 +1249,6 @@
 %    \medskip
 %        
 %    \begin{texshade}{AQP2spec.ALN}
-%       \seqtype{P}
 %       \shadingmode{diverse}
 %       \setends{1}{77..109} \residuesperline*{33}
 %       \featureslarge
@@ -1179,7 +1270,6 @@
 %    \vbox{%
 %    \begin{verbatim}    
 %    \begin{texshade}{AQP2spec.ALN}
-%       \seqtype{P}
 %       \shadingmode{diverse}
 %       \setends{1}{77..109}
 %       \featureslarge
@@ -2124,7 +2214,7 @@
 %       conserved residues, e.\,g.\ |\shadingmode[90]{identical}|. 
 %       \label{Lallmatchspecial}|\allmatchspecial| can also be 
 %       used as a command with or without an optional parameter for
-%       setting the high conservation threshold. As both, option or command 
+%       setting the high conservation threshold. As both, option or command, 
 %       |allmatchspecial| is only active in the \emph{identical} and
 %       \emph{similar} shading modes.
 %       
@@ -2871,6 +2961,58 @@
 %    residues long.
 %    
 %    
+%     \label{Lshowruler}\label{Lhideruler}
+%     \label{Lrulersteps}\label{Lrulercolor}
+%     \label{Lrotateruler}\label{Lunrotateruler}
+%     \label{Lnamerulerpos}
+%     Another possibility to label sequence positions is to switch
+%    on a ruler on the top or at the bottom of the sequence block
+%    using \label{ruler}
+%    |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|. 
+%    The residue ruler of one sequence \meta{seqref} or the consensus 
+%    (declare `|consensus|' as \meta{seqref}) can be 
+%    displayed at \meta{position} |top| or |bottom|.
+%    The ruler is hidden with  |\hideruler|. The steps between two
+%    numbers are set by |\rulersteps{|\meta{number}|}|. If the steps
+%    are set to be very close ($< 4$) or when every position is numbered, the
+%    numbering is automatically rotated by 90$^\circ$. Using |\rotateruler|
+%    and |\unrotateruler| this can be done and undone manually. 
+%    In order to change the
+%    ruler color use the optional parameter or the command 
+%    |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual 
+%    ruler positions can be changed by the user to a string using 
+%    |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| 
+%    (see example on p.\ \pageref{ras}).
+%    
+%    \label{Lgapchar}\label{Lgaprule}
+%    \label{Lgapcolors}\label{gapchar}
+%    Further, the symbol which is displayed in sequence gaps is freely 
+%    selectable with  
+%    |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character
+%    or symbol. If math symbols are to be used math mode must be
+%    activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|.
+%    Note the double curly braces in the last command. Everytime a
+%    `complex' character is used, i.\,e. a character definition consisting 
+%    of more than one letter, it must be braced in order to be interpreted as one 
+%    character. One exception is |\gapchar{rule}|; with this 
+%    parameter lines are drawn in the sequence gaps with a certain 
+%    thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g.
+%    |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by 
+%    |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|.
+%    
+%    There are some discussions whether or not to display gap symbols before
+%    and after the actual sequence. Since v1.3a one can control the
+%    appearance of those gap symbols by the commands
+%    \label{Lshowleadinggaps} \label{Lhideleadinggaps}
+%    |\showleadinggaps| and |\hideleadinggaps|. By default, leading 
+%    gaps are indicated by symbols despite my personal
+%    thinking that it could suggest that 
+%    there are some not displayed residues upstream resp.\ downstream of the 
+%    gap.
+%    
+%    
+%    \subsubsection{Displaying selected residues in the alignment}
+%    
 %    \label{Lsetends}
 %    \TeXshade{} can display a section of the complete alignment
 %    without the need to edit the alignment input file or even 
@@ -2932,55 +3074,64 @@
 %    sequence alignment because the consensus counts every position
 %    including gaps.
 %    
-%     \label{Lshowruler}\label{Lhideruler}
-%     \label{Lrulersteps}\label{Lrulercolor}
-%     \label{Lrotateruler}\label{Lunrotateruler}
-%     \label{Lnamerulerpos}
-%     Another possibility to label sequence positions is to switch
-%    on a ruler on the top or at the bottom of the sequence block
-%    using \label{ruler}
-%    |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|. 
-%    The residue ruler of one sequence \meta{seqref} or the consensus 
-%    (declare `|consensus|' as \meta{seqref}) can be 
-%    displayed at \meta{position} |top| or |bottom|.
-%    The ruler is hidden with  |\hideruler|. The steps between two
-%    numbers are set by |\rulersteps{|\meta{number}|}|. If the steps
-%    are set to be very close ($< 4$) or when every position is numbered, the
-%    numbering is automatically rotated by 90$^\circ$. Using |\rotateruler|
-%    and |\unrotateruler| this can be done and undone manually. 
-%    In order to change the
-%    ruler color use the optional parameter or the command 
-%    |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual 
-%    ruler positions can be changed by the user to a string using 
-%    |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| 
-%    (see example on p.\ \pageref{ras}).
+%    \label{Lsetdomain}
+%    The output can be even further restricted to
+%    individually selected residues, e.g.\ to eliminate uninteresting alignment stretches or
+%    to condense the output, by:
+%    \medskip
 %    
-%    \label{Lgapchar}\label{Lgaprule}
-%    \label{Lgapcolors}\label{gapchar}
-%    Further, the symbol which is displayed in sequence gaps is freely 
-%    selectable with  
-%    |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character
-%    or symbol. If math symbols are to be used math mode must be
-%    activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|.
-%    Note the double curly braces in the last command. Everytime a
-%    `complex' character is used, i.\,e. a character definition consisting 
-%    of more than one letter, it must be braced in order to be interpreted as one 
-%    character. One exception is |\gapchar{rule}|; with this 
-%    parameter lines are drawn in the sequence gaps with a certain 
-%    thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g.
-%    |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by 
-%    |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|.
+%    \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}|
+%    \medskip
 %    
-%    There are some discussions whether or not to display gap symbols before
-%    and after the actual sequence. Since v1.3a one can control the
-%    appearance of those gap symbols by the commands
-%    \label{Lshowleadinggaps} \label{Lhideleadinggaps}
-%    |\showleadinggaps| and |\hideleadinggaps|. By default, leading 
-%    gaps are indicated by symbols despite my personal
-%    thinking that it could suggest that 
-%    there are some not displayed residues upstream resp.\ downstream of the 
-%    gap.
+%    Here, \meta{seqref} denotes the reference sequence by its number or name.
+%    This sequence is used to define the alignment positions \meta{selection} 
+%    to be shown. 
+%    \meta{selection} can have two different formats
+%    depending on whether (a) the user wants to select the positions manually
+%    or (b) \TeXshade{} is supposed to select the residues based on 3D
+%    coordinates provided by a PDB file.
 %    
+%    To select the residues manually, the user provides a position list of
+%    the following format:
+%    \medskip
+%    
+%    \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \medskip
+%
+%    For how to select positions by 3D coordinates
+%    provided by a PDB file, see \ref{Lshaderegion}. 
+%    \medskip
+%    
+%    Examples (see also p.\,\pageref{ident}ff):
+%
+%    \quad|\setdomain{1}{20..80}|
+%    
+%    \quad|\setdomain{consensus}{20..80,100..150,200..220}|
+%    
+%    \quad|\setdomain{AQP1}{point[6]:1FX8.pdb,173[side]}|
+%    
+%    \quad|\setdomain{3}{plane[0.5]:1JN4.pdb,66[CA],73[side],199[CA]}|
+%    \medskip
+%
+%    
+%    It is helpful to show a ruler (probably single-stepped, see p.\,\pageref{Lshowruler}) to 
+%    label the residue positions. 
+%    
+%    The resulting gaps between sequence stretches are marked by a vertical rule, which
+%    can be changed in thickness by 
+%    \medskip
+%
+%    \quad|\domaingaprule{|\meta{thickness}|}|, e.\,g.\
+%    |\domaingaprule{1pt}|. \label{Ldomaingaprule}
+%    \medskip
+%
+%    Also, the colors can be set by 
+%    \medskip
+%
+%    \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}| \label{Ldomaingapcolors}
+%    \medskip
+%
+%     e.\,g.\ |\domaingapcolors{Blue}{Yellow}|.
 %    
 %    
 %    \subsubsection{Hiding, killing, separating and ordering}
@@ -3147,28 +3298,42 @@
 %    
 %    \subsection{Individual shading and labeling of sequence stretches}
 %    
-%    Computer calculated alignment shading is informative---but
-%    even more information can be visualized by manual labeling
+%    Computer calculated conservation shading is informative---but
+%    even more information can be visualized by additional labeling
 %    of positions and regions of interest with different colors,
 %    text styles or graphical marks and descriptive text. All this 
 %    is provided by easy to handle \TeXshade{} commands.
 %    
 %    
-%    \subsubsection{Manual shading of regions and blocks}
+%    \subsubsection{Shading of regions and blocks}
 %    \label{shaderegion}
 %    
 %    \label{Lshaderegion}
 %    Besides the shading calculated by \TeXshade{} any region can be
-%    shaded manually with a color specified by the user. This is very
+%    additionally shaded with a color specified by the user. This is very
 %    useful to highlight secondary protein modification
-%    sites such as phosphorylation or glycosylation sites or longer
-%    motifs for example protein/protein interaction sites.
-%    This is done by the use of the following command:
+%    sites such as phosphorylation or glycosylation sites, or longer
+%    motifs for example protein/protein interaction sites or protein domains.
+%    This is done with the following command:
+%    \medskip
+%    
+%    \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
 %    \medskip
 %    
-%    \quad|\shaderegion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    Here, \meta{seqref} refers to the sequence by its name or number
+%    within the alignment. The 
+%    foreground and background colors can be set with the last two 
+%    parameters. 
+%    \meta{selection} can have two different formats
+%    depending on whether (a) the user wants to select the positions manually
+%    or (b) \TeXshade{} is supposed to select the residues based on 3D
+%    coordinates provided by a PDB file.
+%    
+%    To select the residues manually, the user provides a position list of
+%    the following format:
+%    \medskip
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+%    \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
 %    \medskip
 %    
 %    Example: in order to shade residue number 13 and the region
@@ -3181,22 +3346,80 @@
 %    
 %    If the consensus is to be shaded use |consensus| as 
 %    \meta{seqref}.
+%    \medskip
+%    
+%    In order to select positions based on the 3D structure a PDB
+%    structure file is required. \TeXshade{} can select residues within
+%    a given distance in \AA{} around a point, along a line, or above and
+%    below a plane, which are defined by one to three residues. The points 
+%    can be further specified to be the $\alpha$-carbon atom, i.\,e.\ the
+%    protein backbone, or the most distant atom of the sidechain. Accordingly,
+%    \meta{selection} has one of the formats:
+%    \medskip
+%
+%    \quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}|
+%    \medskip
+%    
+%    \quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}|
+%    \medskip
+%
+%    \vbox{%    
+%    \quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],|
+%    \medskip
+%
+%    \hfill\meta{num3}|[CA/side]}|
+%    }
+%    \medskip
+%    
+%
+%    Example: in order to select and shade as above all residues that are within an 8\ \AA{} 
+%    sphere around the $\alpha$-carbon of residue 81 and the data are
+%    provided in the PDB file |1J4N.pdb|, type:
+%    \medskip
+%    
+%    \quad|\shaderegion{1}{point[8]:1J4N.pdb,81[CA]}{Red}{Green}|
+%    \medskip
+%    
+%    Example: two points denote a line, hence, give two residues to select 
+%    everything within 1\ \AA{} along the line between the $\alpha$-carbon of
+%    residue 81 and the sidechain of residue 168 with:
+%    \medskip
+%    
+%    \quad|\shaderegion{1}{line[1]:1J4N.pdb,81[CA],168[side]}|
+%    \medskip
+%
+%    \hfill|{Red}{Green}|
+%    \medskip
 %    
+%    Definition of a plane follows the same format but requires three points. 
+%    If the optional parameters |[\meta{dist}]| and |[CA/side]| are not given,
+%    \TeXshade{} assumes |[1]| and |[side]|, respectively.
+%
+%    In case one needs the position numbers of the selected residues for usage
+%    in other applications, those can be either printed in the \TeX{} document with
+%    |\printPDBlist{|\meta{selection}|}| or shown during the \TeX{} run with
+%    |\messagePDBlist{|\meta{selection}|}|. The commands can be used outside of the 
+%    \TeXshade{} environment. \label{LprintPDBlist}\label{LmessagePDBlist}
+%    
+%    Both selection formats, i.\,e. a manually given list and the 3D selection,
+%    can be used with |\shadeblock| (see below), 
+%    |\tintregion|, |\tintblock|, |\emphregion|, |\emphblock|, 
+%    |\frameblock| (all in \ref{Lframeblock}), and |\feature| (\ref{Lfeature}).
+%
+%
 %    \label{Lshadeblock}
-%    In analogy to |\shaderegion| which is restricted to one single
-%    sequence |\shadeblock| shades the corresponding region in all 
+%    In analogy to |\shaderegion| which is restricted to a single
+%    sequence, |\shadeblock| shades the corresponding region in all 
 %    other sequences as well
 %    except the consensus. If also the consensus is to be shaded 
 %    define the region using |consensus| as \meta{seqref}.
 %    \medskip
 %    
-%    \quad|\shadeblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+%    \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
 %    \medskip
 %    
 %    
-%    \subsubsection{Emphasizing and tinting regions and blocks}
+%    \subsubsection{Emphasizing, tinting, and framing}
 %    
 %    \label{Lemphregion}\label{Lemphblock}
 %    If it is prefered to keep the calculated shading colors 
@@ -3205,19 +3428,17 @@
 %    such regions:
 %    \medskip
 %    
-%    \quad|\emphregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}|
 %    \medskip   
 %    
 %    and
 %    \medskip
 %    
-%    \quad|\emphblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}|
 %    \medskip   
 %    
+%    For the format possibilities of the \meta{selection} parameter please see \ref{Lshaderegion}.
+%
 %    \label{Lemphdefault}
 %    Which style \TeXshade{} uses for emphasizing regions is defined by 
 %    |\emphdefault{|\meta{style}|}|. Default setting is the
@@ -3233,17 +3454,13 @@
 %    \pageref{hydro}):
 %    \medskip
 %    
-%    \quad|\tintregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}|
 %    \medskip   
 %    
 %    and
 %    \medskip
 %    
-%    \quad|\tintblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}|
 %    \medskip   
 %    
 %    \label{Ltintdefault}
@@ -3257,56 +3474,15 @@
 %    command:\footnote{Thanks to Alan Robinson for inspiration.}
 %    \medskip\label{Lframeblock}
 %
-%    \quad|\frameblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{color}|[|\meta{length}|]}|
+%    \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}|
 %    \medskip
 %
 %    With the optional parameter the default line thickness of the frame can
 %    be changed, example: |\frameblock{1}{10..20,50..70}{Red[2pt]}|
 %
-%    \subsubsection{Hiding blocks of the alignment (experimental!)}
-%    
-%    \label{Lhideblock}
-%    \textit{Be aware that this feature is still highly experimental. There are many instances
-%    in which this command fails. Please be patient until everything is fixed.}
 %
-%    Complete blocks of the alignment incl. all sequences, consensus and labels 
-%    can be hidden, e.g.\ to eliminate uninteresting alignment stretches or
-%    to condense the output, by:
-%    \medskip
-%    
-%    \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}|
-%    \medskip
-%    
-%    Here, \meta{seqref} denotes the sequence by its number of name
-%    which is used to define the alignment positions \meta{start1}..\meta{stop1} 
-%    etc.\ to be hidden. A symbol can be displayed as a 
-%    \meta{label} of the alignment deletion, i.e.\ |circ|, |triangle|, |square|, 
-%    or |none|. A color can be assigned to the label by the optional parameter
-%    \meta{color}. Further, an explanatory text can be displayed above the symbol
-%    \meta{text} with an optional \meta{color}. For how to change the appearance
-%    of the font see p.\pageref{Lsetfont}.
-%    \medskip
-%    
-%    Examples:
 %
-%    \quad|\hideblock{1}{20..80}{circ}{condensed![Red]}|
-%    
-%    \quad|\hideblock{1}{20..80}{triangle[Red]}{hidden block}|
-%    
-%    \quad|\hideblock{AQP1}{20..80}{none[Blue]}{$\Delta$20-80)}|
-%    
-%    \quad|\hideblock{consensus}{20..80,100..150,200..220}{none}{}|
-%    \medskip
 %
-%    It may be advisable to show a ruler (probably single-stepped, see p.\pageref{Lshowruler}) to 
-%    further indicate the alignment deletion. Make sure that there are no 
-%    feature definitions (also frames, emphs, shades, tints) starting or
-%    ending within the hidden block. This may cause messy sequence labels.    
-%    
 %    \subsubsection{Graphical labeling of sequence features}
 %    
 %    \label{feature}
@@ -3317,9 +3493,7 @@
 %    text. It needs five parameters:
 %    \medskip
 %    
-%    \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|
-%    
-%    \quad\quad\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{labelstyle}|}{|\meta{text}|}|
+%    \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}{|\meta{labelstyle}|}{|\meta{text}|}|
 %    \medskip
 %    
 %    In the following paragraphs all possible parameter settings of 
@@ -3346,7 +3520,7 @@
 %    |\bottomspace{-0.1in}|.
 %    
 %    The argument \meta{seqref} and the third 
-%    parameter containing the definitions of the specified regions
+%    parameter containing the selection of the specified residues
 %    are identical to the ones described before in several commands, e.\,g.
 %    |\ruler| (\ref{ruler}) or |\shaderegion| (\ref{shaderegion}). 
 %    
@@ -4895,9 +5069,6 @@
 %    \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}|
 %       \hfill[\pageref{Lseqlength}]
 %    
-%    \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|
-%       \hfill[\pageref{Lsetends}]
-%    
 %    \quad|\showruler[|\meta{color}|]{|\meta{top/bottom}|}{|\meta{seqref}|}|
 %       \hfill[\pageref{Lshowruler}]
 %    
@@ -4936,6 +5107,23 @@
 %       
 %    \vspace{1.5\baselineskip}
 %    
+%    \textbf{Displaying selected residues in the alignment}
+%    \medskip
+%    
+%    \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|
+%       \hfill[\pageref{Lsetends}]
+%    
+%    \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}| (see |\shaderegion| p.\,\pageref{Lshaderegion})
+%       \hfill[\pageref{Lsetdomain}]
+%
+%    \quad|\domaingaprule{|\meta{thickness}|}|
+%       \hfill[\pageref{Lsetdomain}]
+%
+%    \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}|
+%       \hfill[\pageref{Lsetdomain}]
+%
+%    \vspace{1.5\baselineskip}
+%    
 %    \textbf{Hiding, killing, separating and ordering}
 %    \medskip
 %    
@@ -5018,62 +5206,69 @@
 %       
 %    \vspace{1.5\baselineskip}
 %    
+%    \newpage
+%
 %    
 %    \textbf{Individual shading and labeling of sequence stretches}
 %    \medskip
 %    
-%    \quad|\shaderegion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+%       \hfill[\pageref{Lshaderegion}]
+%
+%    \medskip
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
-%       [\pageref{Lshaderegion}]
+%    \quad |{|\meta{selection}|}| =
+%    \medskip%    
 %    
-%    \newpage
+%    \quad\quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
+%    \medskip
+%    
+%    \quad\quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}|
+%    \medskip
+%    
+%    \quad\quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}|
+%    \medskip
+%    
+%    \quad\quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],|
+%    \medskip
 %
-%    \quad|\shadeblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \hfill\meta{num3}|[CA/side]}|
+%    \medskip
+%    
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
-%       [\pageref{Lshadeblock}]
+%    \quad|\printPDBlist{|\meta{selection}|}| \quad|\messagePDBlist{|\meta{selection}|}|
+%       \hfill[\pageref{LprintPDBlist}]
 %    
-%    \quad|\emphregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+%       \hfill[\pageref{Lshadeblock}]
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-%       [\pageref{Lemphregion}]
+%    \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+%       \hfill[\pageref{Lshadeblock}]
 %    
-%    \quad|\emphblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}|
+%       \hfill[\pageref{Lemphregion}]
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-%       [\pageref{Lemphblock}]
+%    \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}|
+%       \hfill[\pageref{Lemphblock}]
 %    
 %    \quad|\emphdefault{|\meta{style}|}|
 %       \hfill[\pageref{Lemphdefault}]
 %    
-%    \quad|\tintregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-%       [\pageref{Ltintregion}]
+%    \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}|
+%       \hfill[\pageref{Ltintregion}]
 %    
-%    \quad|\tintblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-%       [\pageref{Ltintblock}]
+%    \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}|
+%       \hfill[\pageref{Ltintblock}]
 %    
 %    \quad|\tintdefault{|\meta{effect}|}| \qquad\qquad|weak, normal, strong|
 %       \hfill[\pageref{Ltintdefault}]
 %    
-%    \quad|\frameblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}|
+%       \hfill[\pageref{Lframeblock}]
 %    
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{color}|[|\meta{length}|]}|
-%       [\pageref{Lframeblock}]
-%       
-%    \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+%    \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}|
 %
-%    \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}|
-%       [\pageref{Lhideblock}]
-%    
-%    \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|
-%    
-%    \hfill\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{labelstyle}|}{|\meta{text}|}|
-%       [\pageref{Lfeature}]
+%       \hfill |{|\meta{labelstyle}|}{|\meta{text}|}| [\pageref{Lfeature}]
 %    
 %    \begin{tabbing}
 %    \quad\quad\quad|{|\meta{labelstyle}|}|\ \= = |{brace[|\meta{color}|]}|\\
@@ -5090,6 +5285,9 @@
 %               \hspace{5cm}\meta{properties/file/data}|[|\meta{scale}|]}|\\
 %               \hspace{5cm}\meta{properties}: |hydrophobicity|, |charge|,\\
 %               \hspace{7.4cm}|molweight|, |conservation|\\
+%               \hspace{5cm}\meta{scale}: |Gray|, |BlueRed|, |RedBlue|,\\ 
+%               \hspace{6.5cm}|GreenRed|, |RedGreen|, |ColdHot|,\\
+%               \hspace{6.5cm}|HotCold|, |T-Coffee|\\
 %    \end{tabbing}
 %    
 %    \quad|\ttopspace{|\meta{length}|}|
@@ -5430,8 +5628,8 @@
 %    \begin{macrocode}
 %<*texshade>
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
-\message{Package `texshade', Version 1.17 of 2007/06/19.}
+\ProvidesPackage{texshade}[2009/03/09 LaTeX TeXshade (v1.19)]
+\message{Package `texshade', Version 1.19 of 2009/03/09.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -5554,8 +5752,10 @@
 \def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&}
 \def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
 \def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
-\def\gap@char{.} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
 \def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
+\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
 \def\fgroup@num{0} \def\max@seqnumber{0}  \def\@lign@count{0}
 \def\resn@m@tch{upper} \def\ressimm@tch{upper}
 \def\resm@tch{upper}   \def\res@llm@tch{upper}
@@ -6120,6 +6320,8 @@
 \expandafter\xdef\csname cons.Z\endcsname{0}
 \expandafter\xdef\csname cons..\endcsname{0}
 
+\expandafter\xdef\csname cons==\endcsname{0}
+
 \def\c@d@ns{%
 \codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
 \codon{B}{---}
@@ -6872,6 +7074,7 @@
                       \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
                       \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}}
 \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}}
+\def\get@temp#1@{\xdef\temp@{#1}}
 \def\TC@get#1#2@{\xdef\char@num{`#1}
                  \ifnum\char@num=45 \xdef\TC@first@{*}
                  \else
@@ -7016,6 +7219,7 @@
    \ifnum\loopcount<\killseq@count \repeat
    \ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi
    \ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi
+   \ifnum\divref@>0  \xdef\divref@{\csname @rd\divref@\endcsname} \fi
    \loopcount=0
    \loop
       \advance\loopcount by 1
@@ -7506,9 +7710,9 @@
    \xdef\second@{rasmol}
    \ifx\temp@\second@
       \funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up}
-      \funcgroup{Arg, Lys, His}{KR}{Blue}{White}{upper}{up}
-      \funcgroup{Phe, Tyr, Trp}{FY}{MidnightBlue}{White}{upper}{up}
-      \funcgroup{Ala, Gly}{G}{Gray}{White}{upper}{up}
+      \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up}
+      \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up}
+      \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up}
       \funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up}
       \funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up}
       \funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up}
@@ -7574,14 +7778,6 @@
       \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
    \fi\fi
 }
-\def\get@hideregions#1..#2,#3@{%
-   \xdef\hide@true{y}
-   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
-   \xdef\last@{\csname stack@hidereg\seq@\endcsname}
-   \xdef\tmpstack{}
-   \sort@hidestack
-   \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack}
-}
 \def\get@fromemphstack#1;#2;#3;#4@{%
    \xdef\first@{#1} \xdef\second@{#2}
    \xdef\third@{#3} \xdef\last@{#4@}
@@ -7614,6 +7810,40 @@
    \sort@emphstack
    \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
 }
+\def\get@fromdomstack#1;#2;#3@{%
+   \xdef\first@{#1} \xdef\second@{#2}
+   \xdef\last@{#3@}
+}
+\def\sort@domstack{%
+   \expandafter\get@fromdomstack\last@
+   \ifx\first@\ampers@nd
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@}
+   \else
+   \ifnum\st@rt<\second@
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@}
+   \else
+      \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack
+   \fi\fi
+}
+\def\get@domainregions#1..#2,#3@{%
+   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+   \xdef\last@{\stack@dom}
+   \xdef\tmpstack{}
+   \sort@domstack
+   \xdef\stack@dom{\tmpstack}
+}
+\def\get@domain{%
+   \expandafter\get@fromdomstack\last@
+   \ifx\first@\ampers@nd
+   \else
+      \loopcount=\first@
+      \loop
+         \xdef\domain@num@list{\domain@num@list \the\loopcount,}
+         \advance\loopcount by 1
+      \ifnum\loopcount>\second@\else\repeat
+      \get@domain
+   \fi
+}
 \def\getregion@fromtintstack#1{%
    \xdef\temp@{#1}
    \xdef\first@{\csname stack@tintreg\temp@\endcsname}
@@ -7785,6 +8015,132 @@
       \fi%
    \fi%
 }
+
+\def\test@PDB#1:#2,#3,#4,#5,#6@{%
+   \xdef\last@{#1[,]&}\expandafter\opt@color\last@
+   \ifx\f@color\comm@
+      \xdef\PDB@distance{no}
+   \else
+      \xdef\f@color{\f@color .&&@}
+      \expandafter\coord@get\f@color
+      \temp@count=\c@@rd
+      \multiply\temp@count by \temp@count
+      \xdef\PDB@distance{\the\temp@count}
+   \fi
+   \xdef\PDB@hitpos{0}
+   \xdef\PDB@stack{}
+   \xdef\PDB@name{#2}
+   \xdef\PDB@type{point}
+   \ifx\fourth@\PDB@type
+      \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+      \xdef\PDB@refnum@a{\fourth@}
+      \ifx\f@color\C@lpha
+         \xdef\PDB@back@side@a{CA}
+      \else
+         \xdef\PDB@back@side@a{side}
+      \fi
+      \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x}
+      \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+      \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi
+      \load@PDB 
+      \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+   \else
+      \xdef\PDB@type{line}
+      \ifx\fourth@\PDB@type
+         \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+         \xdef\PDB@refnum{\fourth@}
+         \ifx\f@color\C@lpha
+            \xdef\PDB@back@side{CA}
+         \else
+            \xdef\PDB@back@side{side}
+         \fi
+         \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+         \ifnum\PDB@refnum<\fourth@ 
+            \xdef\PDB@refnum@a{\PDB@refnum} 
+            \xdef\PDB@refnum@b{\fourth@}
+            \xdef\PDB@back@side@a{\PDB@back@side}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side@b{CA}
+            \else
+               \xdef\PDB@back@side@b{side}
+            \fi
+         \else
+            \xdef\PDB@refnum@b{\PDB@refnum} 
+            \xdef\PDB@refnum@a{\fourth@}
+            \xdef\PDB@back@side@b{\PDB@back@side}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side@a{CA}
+            \else
+               \xdef\PDB@back@side@a{side}
+            \fi
+         \fi
+         \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+         \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+         \load@PDB 
+         \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+      \else
+         \xdef\PDB@type{plane}
+         \ifx\fourth@\PDB@type
+            \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+            \xdef\PDB@refnum{\fourth@}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side{CA}
+            \else
+               \xdef\PDB@back@side{side}
+            \fi
+            \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+            \ifnum\PDB@refnum<\fourth@ 
+               \xdef\PDB@refnum@a{\PDB@refnum} 
+               \xdef\PDB@refnum@b{\fourth@}
+               \xdef\PDB@back@side@a{\PDB@back@side}
+               \ifx\f@color\C@lpha
+                  \xdef\PDB@back@side@b{CA}
+               \else
+                  \xdef\PDB@back@side@b{side}
+               \fi
+            \else
+               \xdef\PDB@refnum@b{\PDB@refnum} 
+               \xdef\PDB@refnum@a{\fourth@}
+               \xdef\PDB@back@side@b{\PDB@back@side}
+               \ifx\f@color\C@lpha
+                  \xdef\PDB@back@side@a{CA}
+               \else
+                  \xdef\PDB@back@side@a{side}
+               \fi
+            \fi
+            \xdef\last@{#5[,]&}\expandafter\opt@color\last@
+            \xdef\PDB@refnum{\fourth@}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side{CA}
+            \else
+               \xdef\PDB@back@side{side}
+            \fi
+            \ifnum\PDB@refnum>\PDB@refnum@b
+               \xdef\PDB@refnum@c{\PDB@refnum}
+               \xdef\PDB@back@side@c{\PDB@back@side}
+            \else
+               \ifnum\PDB@refnum>\PDB@refnum@a
+                  \xdef\PDB@refnum@c{\PDB@refnum@b}
+                  \xdef\PDB@back@side@c{\PDB@back@side@b}
+                  \xdef\PDB@refnum@b{\PDB@refnum}
+                  \xdef\PDB@back@side@b{\PDB@back@side}
+               \else
+                  \xdef\PDB@refnum@c{\PDB@refnum@b}
+                  \xdef\PDB@back@side@c{\PDB@back@side@b}
+                  \xdef\PDB@refnum@b{\PDB@refnum@a}
+                  \xdef\PDB@back@side@b{\PDB@back@side@a}
+                  \xdef\PDB@refnum@a{\PDB@refnum}
+                  \xdef\PDB@back@side@a{\PDB@back@side}
+               \fi
+            \fi
+            \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+            \load@PDB 
+            \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+         \fi
+      \fi
+   \fi
+}
+
 \def\test@fill#1:#2:#3&{%
    \xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@%
    \xdef\second@@{\fourth@}%
@@ -7961,6 +8317,7 @@
     \expandafter\xdef\csname \prfx grpZ\endcsname{-26}
     \expandafter\xdef\csname \prfx grp-\endcsname{-999}
     \expandafter\xdef\csname \prfx grp.\endcsname{-999}
+    \expandafter\xdef\csname \prfx grp=\endcsname{-999}
 }
 \def\inactivate@chars{%
    \catcode`\#=12
@@ -7975,9 +8332,15 @@
 \def\romancount{\@roman\loopcount}
 \def\Romancount{\@Roman\loopcount}
 \def\cut@name#1.#2@{\global\xdef\file@n@me{#1}}
+\def\coord@get#1.#2#3@{%
+   \xdef\temp@{#2}
+   \ifx\temp@\ampers@nd \xdef\temp@{0} \fi
+   \xdef\c@@rd{#1\temp@}
+}
 \def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{%
     \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3}  \xdef\fourth@{#4}
-    \xdef\fifth@{#5} \xdef\sixth@{#6}  \xdef\seventh@{#7}\xdef\eighth@{#8}}
+    \xdef\fifth@{#5} \xdef\sixth@{#6}  \xdef\seventh@{#7}\xdef\eighth@{#8}
+    \xdef\nineth@{#9}}
 \def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}}
 \def\write@PHDsec{%
  \expandafter\get@sim\last@
@@ -8945,7 +9308,7 @@
   \xdef\fourth@{#2,&,@}
   \expandafter\get@triplet\fourth@
    \fi}
-   
+\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}}   
 \def\get@name@number{%
    \xdef\second@{n}
    \loopcount=0
@@ -8961,7 +9324,323 @@
       \xdef\first@{1}
    \fi
 }
+ 
+\def\calc@distance@point{%
+   \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax 
+   \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+   \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax 
+   \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+   \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax 
+   \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+   \advance\loopcount by \y@distance\relax
+   \advance\loopcount by \x@distance\relax
+   \ifnum\loopcount > \PDB@distance \else 
+      \loopcount=\PDB@hitpos \advance\loopcount by 1 
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
+\def\calc@distance@line{%
+   \loopcount=\x@coord\relax \multiply\loopcount by \x@orient
+   \temp@count=\y@coord \relax \multiply\temp@count by \y@orient
+   \advance\loopcount by \temp@count 
+   \temp@count=\z@coord \relax \multiply\temp@count by \z@orient
+   \advance\loopcount by \temp@count 
+   \advance\loopcount by -\c@nst@ 
+   \xdef\z@hler{\the\loopcount}
+   \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a
+   \advance\loopcount by -\x@coord
+   \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+   \loopcount=\z@hler   
+   \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a
+   \advance\loopcount by -\y@coord
+   \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+   \loopcount=\z@hler   
+   \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a
+   \advance\loopcount by -\z@coord
+   \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+   \advance\loopcount by \y@distance\relax
+   \advance\loopcount by \x@distance\relax
+   \ifnum\loopcount > \PDB@distance \else 
+      \loopcount=\PDB@hitpos \advance\loopcount by 1 
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
+
+\def\intr@@t{%
+   \loopcount=\r@@t
+   \temp@count=1
+   \loop
+      \advance\loopcount by \temp@count
+      \divide\loopcount by 2
+      \temp@count=\r@@t
+      \divide\temp@count by \loopcount
+   \ifnum\loopcount>\temp@count\repeat
+}
+
+
+\def\calc@distance@plane{%
+   \loopcount=\x@coord\relax
+   \multiply\loopcount by \x@orient
+   \temp@count=\y@coord \relax
+   \multiply\temp@count by \y@orient
+   \advance\loopcount by \temp@count 
+   \temp@count=\z@coord \relax
+   \multiply\temp@count by \z@orient
+   \advance\loopcount by \temp@count
+   \advance\loopcount by \c@nst@
+   \divide\loopcount by \f@ct@r  
+   \multiply\loopcount by \loopcount
+   \ifnum\loopcount > \PDB@distance \else 
+      \loopcount=\PDB@hitpos \advance\loopcount by 1 
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
    
+\def\load@PDB{%
+    \bgroup
+    \immediate\openin\structurefile = \PDB@name\relax
+    \ifeof\structurefile
+      \PackageError{TeXshade}
+      {File `\PDB@name' not found}
+      {\MessageBreak
+       The file you specified is missing or you have \MessageBreak
+       misspelled it. \MessageBreak\MessageBreak
+       No PDB domain labeling will be displayed. \MessageBreak
+       Type <return> to proceed. \MessageBreak
+       Type X <return> to quit. \MessageBreak
+}
+       \immediate\closein\structurefile\egroup
+    \else
+    \message{<reading PDB: \PDB@name>}
+    \xdef\first@{}
+    \loop
+       \read\structurefile to \readline
+       \xdef\test@{\expandafter\string\readline}
+       \ifx\test@\par@
+       \else
+          \xdef\structureline{\readline & & & & & & & & &@}
+          \expandafter\struc@get\structureline
+          \ifx\first@\@TOM 
+             \ifx\PDB@back@side@a\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@a
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@a
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@a
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@a
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+                   \fi
+                \fi
+             \fi
+             \ifx\PDB@back@side@b\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@b
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@b
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@b
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@b
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+                   \fi
+                \fi
+             \fi
+             \ifx\PDB@back@side@c\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@c
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@c
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@c
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@c
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+                   \fi
+                \fi
+             \fi
+          \fi
+       \fi
+    \ifeof\structurefile \else\repeat
+    \closein\structurefile
+    \ifx\PDB@type\@line@
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount}
+       \loopcount=\xref@coord@a \multiply\loopcount by \x@orient
+       \temp@count=\yref@coord@a \multiply\temp@count by \y@orient
+       \advance\loopcount by \temp@count
+       \temp@count=\zref@coord@a \multiply\temp@count by \z@orient
+       \advance\loopcount by \temp@count 
+       \xdef\c@nst@{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \x@orient
+       \temp@count=\y@orient \multiply\temp@count by \y@orient
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \z@orient
+       \advance\loopcount by \temp@count
+       \xdef\f@ct@r{\the\loopcount}
+    \fi
+    \ifx\PDB@type\@plane@
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount}
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount}
+       \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s
+       \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount}
+       \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s
+       \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount}
+       \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s
+       \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \xref@coord@a
+       \temp@count=\y@orient \multiply\temp@count by \yref@coord@a
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \zref@coord@a
+       \advance\loopcount by \temp@count 
+       \multiply\loopcount by -1\relax 
+       \xdef\c@nst@{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \loopcount
+       \temp@count=\y@orient \multiply\temp@count by \temp@count
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \temp@count
+       \advance\loopcount by \temp@count
+       \xdef\r@@t{\the\loopcount} \intr@@t
+       \xdef\f@ct@r{\the\loopcount}
+    \fi
+    \immediate\openin\structurefile = \PDB@name\relax
+    \xdef\first@{}
+    \loop
+       \read\structurefile to \readline
+       \xdef\test@{\expandafter\string\readline}
+       \ifx\test@\par@
+       \else
+          \xdef\structureline{\readline & & & & & & & & &@}
+          \expandafter\struc@get\structureline
+          \ifx\first@\@TOM
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                      \xdef\PDB@pos{\fifth@}
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd}
+                \else
+                      \xdef\PDB@pos{\sixth@}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd}
+                \fi
+                \ifnum\PDB@hitpos=\PDB@pos
+                \else
+                   \ifx\PDB@type\@point@
+                      \calc@distance@point
+                   \else
+                      \ifx\PDB@type\@line@
+                         \calc@distance@line
+                      \else
+                         \ifx\PDB@type\@plane@
+                            \calc@distance@plane
+                         \fi
+                      \fi
+                   \fi
+                \fi
+          \fi
+       \fi
+    \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@}
+    \else\repeat
+    \closein\structurefile
+    
+   \fi
+   \egroup
+ }
+ 
+
 
 %%%%% Definition of user commands
 
@@ -9051,6 +9730,34 @@
       \separationline{\the\loopcount}
    \ifnum\loopcount<\seq@count\repeat
    \fi}
+\def\printPDBlist#1{%
+     \xdef\list@{}
+     \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+     \xdef\first@{\list@ &}
+     \ifx\first@\ampers@nd
+     \else
+        \xdef\first@{\list@ @} 
+        \loop
+           \expandafter\get@item\first@
+           \fourth@
+        \ifx\first@@\ampers@nd\else{,\ }\repeat
+     \fi
+}
+\def\messagePDBlist#1{%
+     \xdef\list@{}
+     \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+     \xdef\first@{\list@ &}
+     \ifx\first@\ampers@nd
+     \else
+        \message{(#1:}
+        \xdef\first@{\list@ @}%
+        \loop%
+           \expandafter\get@item\first@%
+           \message{\fourth@}%
+        \ifx\first@@\ampers@nd\else\repeat%
+        \message{)}
+     \fi
+}
 \def\shaderegion#1#2#3#4{%
    \regionalshadetrue
    \xdef\seq@{#1}
@@ -9068,6 +9775,7 @@
      \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
      \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ 
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@regions\list@
@@ -9091,6 +9799,7 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@tintregions\list@
@@ -9131,6 +9840,7 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@emphregions\list@
@@ -9155,29 +9865,13 @@
    \else
      \xdef\@ll{#3}
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@frameregions\list@
      \ifx\list@\ampers@nd\else\repeat
    \fi
 }
-\def\hideblock#1#2#3#4{%
-   \xdef\seq@{#1}
-   \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
-   \xdef\first@{\seq@ @} \expandafter\check@letter\first@
-   \xdef\first@{\seq@}
-   \ifletter \get@name@number \xdef\seq@{\first@} \fi
-   \ifnum\seq@>\seq@count
-     \message{<Ignored seq `\seq@' in \noexpand\hideblock>}
-   \else
-     \xdef\@ll{#3} \xdef\text@{#4}
-     \xdef\list@{#2,&}
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@hideregions\list@
-     \ifx\list@\ampers@nd\else\repeat
-   \fi 
-}
 \def\bargraphstretch#1{\def\b@r@stretch{#1}}
 \def\colorscalestretch#1{\def\sc@le@stretch{#1}}
 \def\rm@@measure#1#2@{%
@@ -9539,7 +10233,7 @@
    \ifx\second@@\last@
       \xdef\list@{#3,&}
       \xdef\style@{#4}
-      \xdef\f@text@{#5}
+      \def\f@text@{#5}
       \do@bargraph
       \xdef\temp@{bottom}
       \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi
@@ -9554,11 +10248,14 @@
    \ifx\second@@\last@
       \xdef\list@{#3,&}
       \xdef\style@{#4}
-      \xdef\f@text@{#5}
+      \def\f@text@{#5}
       \do@colorgraph
    \else
-   \xdef\f@text@{#5}
+   \xdef\f@@color{\f@color}
    \xdef\list@{#3,&}
+   \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
+   \def\f@text@{#5}
+   \xdef\f@color{\f@@color}
    \xdef\temp@{#4&}
    \ifx\temp@\ampers@nd
       \xdef\style@{&}
@@ -9636,7 +10333,9 @@
       \fi
       \fi
    \fi
+   \loopcount=0
    \loop
+      \advance\loopcount by 1\relax
       \xdef\list@{\list@ @}
       \expandafter\get@fregions\list@
    \ifx\list@\ampers@nd\else\repeat
@@ -9694,7 +10393,23 @@
    \def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next}
    \futurelet\l@@k\decide@}
 \def\numberingwidth#1{\def\num@width{#1}}
-\def\charstretch#1{\def\char@stretch{#1}}
+\def\charstretch#1{%
+   \def\char@stretch{#1}
+   \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd
+   \multiply \loopcount by 7
+   \divide \loopcount by 10
+   \ifnum\loopcount<10
+      \xdef\temp@{0\the\loopcount @}
+   \else
+      \xdef\temp@{\the\loopcount @}
+   \fi
+   \expandafter\decimal@B\temp@
+   \ifnum\loopcount>99
+      \xdef\char@stretch@W{#1}
+   \else
+      \xdef\char@stretch@W{\temp@}
+   \fi
+}
 \def\linestretch#1{\def\line@stretch{#1}}
 \def\logostretch#1{%
    \def\logo@stretch{#1}
@@ -9826,6 +10541,7 @@
    \ifx\first@\second@\def\gap@char{o}
    \else\def\gap@char{#1}\fi}
 \def\gaprule#1{\def\gap@rulethick{#1}}
+\def\domaingaprule#1{\def\domgap@rulethick{#1}}
 \newcommand{\setends}[3][&]{%
   \xdef\start@seq{#2}
   \xdef\temp@{consensus}
@@ -10298,9 +11014,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@family{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@family{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@family{\third@}
    \else
@@ -10318,9 +11031,8 @@
       \xdef\residues@family{\third@}
       \xdef\legend@family{\third@}
       \xdef\label@family{\third@}
-      \xdef\hideblock@family{\third@}
       \xdef\ruler@family{\second@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setseries#1#2{%
@@ -10363,9 +11075,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@series{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@series{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@series{\third@}
    \else
@@ -10379,9 +11088,8 @@
       \xdef\namestext@series{\third@}
       \xdef\residues@series{\third@}
       \xdef\legend@series{\third@}
-      \xdef\hideblock@series{\third@}
       \xdef\label@series{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setshape#1#2{%
@@ -10432,9 +11140,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@shape{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@shape{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@shape{\third@}
    \else
@@ -10448,9 +11153,8 @@
       \xdef\namestext@shape{\third@}
       \xdef\residues@shape{\third@}
       \xdef\legend@shape{\third@}
-      \xdef\hideblock@shape{\third@}
       \xdef\label@shape{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setsize#1#2{%
@@ -10486,20 +11190,6 @@
    \ifx\first@\temp@
       \def\legend@size{\csname #2\endcsname}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@
-      \xdef\temp@@{#2}
-      \xdef\temp@{huge}
-      \ifx\temp@\temp@@
-         \def\hideblock@size{\csname LARGE\endcsname}
-      \else
-      \xdef\temp@{Huge}
-      \ifx\temp@\temp@@
-         \def\hideblock@size{\csname LARGE\endcsname}
-      \else
-         \def\hideblock@size{\csname #2\endcsname}
-      \fi\fi
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@
       \def\label@size{\csname #2\endcsname}
@@ -10518,11 +11208,10 @@
       \def\numbertext@size{\csname #2\endcsname}
       \def\namestext@size{\csname #2\endcsname}
       \def\legend@size{\csname #2\endcsname}
-      \def\hideblock@size{\csname #2\endcsname}
       \def\label@size{\csname #2\endcsname}
       \def\residues@size{\csname #2\endcsname}
       \xdef\res@size{#2}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \xdef\temp@{Huge}
    \ifx\temp@\res@size
       \def\bottomruler@size{\csname Large\endcsname}
@@ -10706,25 +11395,6 @@
 \def\legendLARGE       {\setsize{legend}{LARGE}}
 \def\legendhuge        {\setsize{legend}{huge}}
 \def\legendHuge        {\setsize{legend}{Huge}}
-\def\hideblockrm{\setfamily{hideblock}{rm}}
-\def\hideblocksf{\setfamily{hideblock}{sf}}
-\def\hideblocktt{\setfamily{hideblock}{tt}}
-\def\hideblockmd{\setseries{hideblock}{md}}
-\def\hideblockbf{\setseries{hideblock}{bf}}
-\def\hideblockup{\setshape {hideblock}{up}}
-\def\hideblockit{\setshape {hideblock}{it}}
-\def\hideblocksl{\setshape {hideblock}{sl}}
-\def\hideblocksc{\setshape {hideblock}{sc}}
-\def\hideblocktiny        {\setsize{hideblock}{tiny}}
-\def\hideblockscriptsize  {\setsize{hideblock}{scriptsize}}
-\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}}
-\def\hideblocksmall       {\setsize{hideblock}{small}}
-\def\hideblocknormalsize  {\setsize{hideblock}{normalsize}}
-\def\hideblocklarge       {\setsize{hideblock}{large}}
-\def\hideblockLarge       {\setsize{hideblock}{Large}}
-\def\hideblockLARGE       {\setsize{hideblock}{LARGE}}
-\def\hideblockhuge        {\setsize{hideblock}{LARGE}}
-\def\hideblockHuge        {\setsize{hideblock}{LARGE}}
 \def\rulerrm{\setfamily{ruler}{rm}}
 \def\rulersf{\setfamily{ruler}{sf}}
 \def\rulertt{\setfamily{ruler}{tt}}
@@ -10817,6 +11487,12 @@
                                 \expandafter\def\csname fg@textcolor*\endcsname{#1}\fi
                              \ifx\second@\last@\else\def\gap@bg{#2}
                                 \expandafter\def\csname fg@color*\endcsname{#2}\fi}
+\def\domaingapcolors#1#2     {\xdef\first@{#1&}\xdef\second@{#2&}
+                             \xdef\last@{\ampers@nd}
+                             \ifx\first@\last@\else\def\domgap@fg{#1}
+                                \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi
+                             \ifx\second@\last@\else\def\domgap@bg{#2}
+                                \expandafter\def\csname fg@color!\endcsname{#2}\fi}
 \def\shadebox#1{%
    \xdef\first@{White}%
    \xdef\third@{#1}%
@@ -11289,6 +11965,24 @@
    \fi
 }
 
+\def\setdomain#1#2{%
+   \xdef\first@{#1}
+   \xdef\temp@{consensus}
+   \ifx\first@\temp@ \xdef\domain@seq{0}
+   \else
+      \xdef\first@{#1 @} \expandafter\check@letter\first@
+      \xdef\first@{#1}   \ifletter \get@name@number \fi
+      \xdef\domain@seq{\csname @rd\first@\endcsname}%
+   \fi
+   \xdef\list@{#2,&}
+   \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+   \loop
+        \xdef\list@{\list@ @}
+        \expandafter\get@domainregions\list@
+   \ifx\list@\ampers@nd\else\repeat
+   \xdef\dom@in{y}
+}
+
 %%%%%  Calculate consensus
 
 \def\check@sim{%
@@ -11354,7 +12048,7 @@
    \fi
  \else
     \newresfalse
-    \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t}
+%    \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t}  %%%%% or \equ@l for domains!!!
  \fi
 
  \ifnewres
@@ -11448,13 +12142,29 @@
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
                 \csname seq\the\loopcount\endcsname3\gap@char}
             \else
+             \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l
+              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                 \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y}
+             \else
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
                 \csname seq\the\loopcount\endcsname%
                 3\csname res\the\loopcount\endcsname}
              \fi
+             \fi
           \else
            \xdef\first@{\csname res\the\loopcount\endcsname}
-           \ifx\first@\d@t
+           \ifx\first@\equ@l
+             \def\first@{\dom@char} \def\third@{9}
+             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+             \xdef\first@{=\first@}\fi
+             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+             \xdef\first@{,\first@}\fi
+             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                              \csname seq\the\loopcount\endcsname\third@\first@} \xdef\g@p{y}
+           \else
+             \ifx\first@\d@t
                  \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                       <\csname seq@start\the\loopcount\endcsname
                     \ifsh@wg@ps
@@ -11474,27 +12184,28 @@
                     \fi
                     \fi
                  \fi
-             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
-                \xdef\first@{=\first@}\fi
-             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
-                \xdef\first@{,\first@}\fi
-             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname\third@\first@}
-           \else
-             \ifnum\divref@=\loopcount\else 
-             \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
-             \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-             \else \xdef\first@{\resn@m@tch} \fi\fi\fi
-             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
-             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
                 \xdef\first@{,\first@}\fi
-             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname3\first@}
+                \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                                 \csname seq\the\loopcount\endcsname\third@\first@}
+             \else
+               \ifnum\divref@=\loopcount\else 
+               \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
+               \xdef\low@up{upper} \ifx\resn@m@tch\low@up
+               \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+               \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                  \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                  \xdef\first@{=\first@}\fi
+               \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                  \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                  \xdef\first@{,\first@}\fi
+               \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                  \csname seq\the\loopcount\endcsname3\first@}
+             \fi
            \fi
           \fi
        \ifnum\loopcount<\seq@count \repeat
@@ -11507,9 +12218,13 @@
        \expandafter\ifx\csname emph@seq0\endcsname\y@
           \expandafter\xdef\csname emph@seq0\endcsname{n}
           \xdef\first@{,\first@}\fi
-       \xdef\consensus{\consensus 4\first@}
-       \expandafter\ifx\csname res\cons@num\endcsname\d@t
+       \ifx\g@p\y@
+          \xdef\consensus{\consensus 8{}} 
+       \else
+          \xdef\consensus{\consensus 4\first@} 
+          \expandafter\ifx\csname res\cons@num\endcsname\d@t
           \else\xdef\constopo{\constopo 0}\fi
+       \fi
     \else
      \ifnum\cons@num>0
        \xdef\tmp@{\csname res\cons@num\endcsname}
@@ -11525,6 +12240,7 @@
         \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -11532,8 +12248,7 @@
                 \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
                 \xdef\first@{,\first@}\fi
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname%
-                3\first@}
+                \csname seq\the\loopcount\endcsname3\first@} 
         \else
           \xdef\first@{\csname res\the\loopcount\endcsname}
           \xdef\last@{\csname res\the\loopcount\endcsname}
@@ -11544,6 +12259,9 @@
               \xdef\low@up{upper} \ifx\ressimm@tch\low@up
               \else \xdef\first@{\ressimm@tch} \fi\fi\fi
           \else
+            \ifx\first@\equ@l
+              \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y}
+            \else
               \ifx\first@\d@t
                  \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                       <\csname seq@start\the\loopcount\endcsname
@@ -11571,6 +12289,7 @@
                  \xdef\low@up{upper} \ifx\resn@m@tch\low@up
                  \else \xdef\first@{\resn@m@tch} \fi\fi\fi
               \fi
+            \fi
           \fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -11592,8 +12311,12 @@
      \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
-     \xdef\consensus{\consensus5\first@}
-     \xdef\constopo{\constopo 1}
+     \ifx\g@p\y@
+        \xdef\consensus{\consensus 8{}}
+     \else
+        \xdef\consensus{\consensus5\first@}
+        \xdef\constopo{\constopo 1}
+     \fi
     \fi
  \else
  \iffuncmode
@@ -11601,6 +12324,17 @@
     \loop
        \advance\loopcount by 1
        \xdef\first@{\csname res\the\loopcount\endcsname}
+       \ifx\first@\equ@l
+          \def\first@{\dom@char} \def\third@{!}  \xdef\g@p{y}
+          \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{=\first@}\fi
+          \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{,\first@}\fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+             \csname seq\the\loopcount\endcsname\third@\first@}
+       \else
        \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -11642,6 +12376,7 @@
           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
              \csname seq\the\loopcount\endcsname0\first@}
        \fi
+       \fi
     \ifnum\loopcount<\seq@count \repeat
  \else
     \loopcount=0
@@ -11651,6 +12386,7 @@
         \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char}  \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -11662,6 +12398,17 @@
                 3\first@}
         \else
          \xdef\first@{\csname res\the\loopcount\endcsname}
+         \ifx\first@\equ@l
+            \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y}
+           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{=\first@}\fi
+           \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{,\first@}\fi
+           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+              \csname seq\the\loopcount\endcsname\third@\first@}
+         \else
          \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -11704,6 +12451,7 @@
            \expandafter\xdef\csname seq\the\loopcount\endcsname{%
              \csname seq\the\loopcount\endcsname3\first@}
          \fi
+         \fi
         \fi
     \ifnum\loopcount<\seq@count \repeat
     \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
@@ -11715,8 +12463,12 @@
     \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
-    \xdef\consensus{\consensus 4\first@}
-    \xdef\constopo{\constopo 0}
+    \ifx\g@p\y@
+       \xdef\consensus{\consensus 8{}}
+    \else
+       \xdef\consensus{\consensus 4\first@}
+       \xdef\constopo{\constopo 0}
+    \fi
  \fi\fi}
 
 \def\c@nserved{%
@@ -11728,6 +12480,7 @@
     \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -11766,6 +12519,7 @@
     \xdef\low@up{upper} \ifx\resn@m@tch\low@up
     \else \xdef\first@{\resn@m@tch} \fi\fi\fi
     \fi
+    \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y} \fi
     \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -11807,9 +12561,13 @@
  \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 5\first@}
- \xdef\constopo{\constopo 2}}
-
+ \ifx\g@p\y@
+    \xdef\consensus{\consensus 8{}}
+ \else
+    \xdef\consensus{\consensus 5\first@}
+    \xdef\constopo{\constopo 2}
+ \fi}
+ 
 \def\allm@tch{%
  \xdef\tmp@{\csname res\cons@seq\endcsname}
  \loopcount=0
@@ -11819,6 +12577,7 @@
     \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -11862,6 +12621,7 @@
     \xdef\low@up{upper} \ifx\resn@m@tch\low@up
     \else \xdef\first@{\resn@m@tch} \fi\fi\fi
     \fi
+    \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y} \fi
     \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -11903,8 +12663,12 @@
  \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 6\first@}
- \xdef\constopo{\constopo 3}}
+ \ifx\g@p\y@
+    \xdef\consensus{\consensus 8{}}
+ \else
+    \xdef\consensus{\consensus 6\first@}
+    \xdef\constopo{\constopo 3}
+ \fi}
 
 \def\functi@nal{%
      \ifnum\cons@num>0
@@ -11930,6 +12694,9 @@
                 0\first@}
         \else
         \xdef\first@{\csname res\the\loopcount\endcsname}
+         \ifx\first@\equ@l
+            \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+         \else
          \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -11961,6 +12728,7 @@
               \xdef\low@up{upper} \ifx\resn@m@tch\low@up
               \else \xdef\first@{\resn@m@tch} \fi\fi
          \fi
+         \fi
         \fi
         \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -11980,6 +12748,7 @@
      \xdef\first@{\csname res\the\loopcount\endcsname}
      \xdef\second@{\csname funcgrp\first@\endcsname}
      \ifnum\second@<0 \xdef\second@{0} \fi
+     \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!}  \xdef\g@p{y} \fi
      \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -12030,19 +12799,11 @@
 
 \def\T@coffee@shade{%
    \loopcount=0
-   \expandafter\ifx\csname tint@seq0\endcsname\y@
-                \expandafter\xdef\csname tint@seq0\endcsname{n}
-                \xdef\first@{=\first@}\fi
-   \expandafter\ifx\csname emph@seq0\endcsname\y@
-                \expandafter\xdef\csname emph@seq0\endcsname{n}
-                \xdef\first@{,\first@}\fi
-   \xdef\second@{\csname TC@num0\endcsname}
-   \xdef\consensus{\consensus\second@\n@m@tch}
-   \xdef\constopo{\constopo\second@}
    \loop
      \advance\loopcount by 1
      \xdef\first@{\csname res\the\loopcount\endcsname}
      \xdef\second@{\csname TC@num\the\loopcount\endcsname}
+     \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!}  \xdef\g@p{y} \fi
      \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -12086,7 +12847,22 @@
                 \csname seq\the\loopcount\endcsname%
                 \second@\first@}
      \fi
-   \ifnum\loopcount<\seq@count \repeat}
+   \ifnum\loopcount<\seq@count \repeat
+   \xdef\first@{\csname res0\endcsname}
+   \expandafter\ifx\csname tint@seq0\endcsname\y@
+                \expandafter\xdef\csname tint@seq0\endcsname{n}
+                \xdef\first@{=\first@}\fi
+   \expandafter\ifx\csname emph@seq0\endcsname\y@
+                \expandafter\xdef\csname emph@seq0\endcsname{n}
+                \xdef\first@{,\first@}\fi
+   \xdef\second@{\csname TC@num0\endcsname}
+   \ifx\g@p\y@
+      \xdef\consensus{\consensus 8{}}
+   \else
+      \xdef\consensus{\consensus\second@\n@m@tch}
+      \xdef\constopo{\constopo\second@}
+   \fi
+   }
 
 \def\getregion@fromstack@first{%
       \expandafter\getregion@fromstack{\the\loopcount}
@@ -12129,7 +12905,6 @@
             \fi
          \fi\fi
       \ifnum\loopcount<\seq@count \repeat
-      \ifx\hide@now\n@
       \loopcount=0
       \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@
       \else
@@ -12149,7 +12924,6 @@
                               &\csname shade@style\the\loopcount\endcsname)}
          \fi
       \ifnum\loopcount<\seq@count \repeat
-      \fi
 }
 
 \def\getregion@fromemphstack@first{%
@@ -12512,13 +13286,13 @@
          \xdef\cons@val{\csname TC@num0\endcsname}
          \if\cons@val * 
             \xdef\cons@val{99}
-         \fi   \message{(b(\cons@val)b)}
+         \fi
       \fi
       \ifx\T@coffee@ccons\y@
          \xdef\cons@val{\csname TC@num0\endcsname}
          \if\cons@val * 
             \xdef\cons@val{99}
-         \fi   \message{(c(\cons@val)c)}
+         \fi
       \fi
    \fi
 }
@@ -13417,11 +14191,25 @@
 %      \advance\pos@count by 1
 }
 
+\def\add@to@rule@tens{%
+    \advance\innerloopcount by \ruler@step\relax
+    \ifnum\innerloopcount=0 
+          \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+    \fi
+    \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens
+    \else
+       \xdef\rule@tens{\the\innerloopcount}
+    \fi
+}
+
+
 \def\c@nsensus{%
  \ifnum\pos@count>\res@perline
     \else
     \loopcount=0
-    \global\advance\cons@count by 1\relax
+    \ifx\g@p\n@
+       \global\advance\cons@count by 1\relax
+    \fi
     \ifnum\cons@count=0\relax
        \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
     \fi
@@ -13430,21 +14218,6 @@
             \expandafter\TC@get\TC@line
     \fi
     \expandafter\xdef\csname res@count0\endcsname{\the\cons@count}
-    \ifx\hide@true\y@
-    \expandafter\ifx\csname hidestart0\endcsname\ampers@nd
-    \else
-       \expandafter\ifnum\csname hidestart0\endcsname>\cons@count
-       \else
-          \expandafter\ifnum\csname hidestop0\endcsname<\cons@count
-          \else
-             \xdef\hide@now{y} \xdef\eighth@{0}
-          \fi
-          \expandafter\ifnum\csname hidestop0\endcsname=\cons@count
-             \getregion@fromhidestack{0}
-          \fi
-    \fi
-    \fi
-    \fi
     \loop
          \advance\loopcount by 1
          \ifT@coffee
@@ -13452,53 +14225,42 @@
             \expandafter\TC@get\TC@line
             \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname}
          \fi
-         \xdef\seq@line{\csname sequence\the\loopcount\endcsname}
+         \xdef\seq@line{\csname sequence\the\loopcount\endcsname} 
          \expandafter\residue@get\seq@line
          \xdef\first@{\csname res\the\loopcount\endcsname}
          \innerloopcount=\csname res@num\first@\endcsname
          \advance\innerloopcount by 1
          \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount}
          \expandafter\check@char\first@
+         \ifx\dom@in\y@ %%%%%%%%%%%*****
+                \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+                \expandafter\get@dom@count\temp@
+                \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}    
+         \fi            %%%%%%%%%%%*****
          \ifletter
-             \res@count=\csname res@count\the\loopcount\endcsname
-             \advance\res@count by 1
-             \ifnum\res@count=0\relax
-                \ifx\allow@zero\n@ \advance\res@count by 1 \fi
-             \fi
-             \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
-             \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
-             \ifx\hide@true\y@
-             \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd
-             \else
-             \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count
+             \ifx\dom@in\y@
              \else
-                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count
-                \else
-                   \xdef\hide@now{y}\xdef\eighth@{\the\loopcount}
-                \fi
-                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count
-                   \xdef\first@@{\first@}
-                   \expandafter\getregion@fromhidestack{\the\loopcount}
-                   \xdef\first@{\first@@}
-                \fi
-             \fi
+                \res@count=\csname res@count\the\loopcount\endcsname
+                \advance\res@count by 1
+                \ifnum\res@count=0\relax
+                   \ifx\allow@zero\n@ \advance\res@count by 1 \fi
              \fi
              \fi
+             \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+             \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
              \ifnum\loopcount=\rule@num\relax 
+              \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens 
+                 \innerloopcount=\rule@tens \add@to@rule@tens
+              \fi  
               \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens
                 \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
                    \xdef\temp@{\rule@tens}
                 \else
                    \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
                 \fi
-                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
-                \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
-                \ifnum\innerloopcount=0 
-                   \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
-                \fi
-                \xdef\rule@tens{\the\innerloopcount}
+                \xdef\ruler@{\ruler@ !<\temp@>}
               \else
-                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+                \xdef\ruler@{\ruler@ -}
               \fi
               \xdef\temp@{\csname res@count\rule@num\endcsname}
               \expandafter\ifx\csname alt@ruler\temp@\endcsname\relax
@@ -13506,7 +14268,6 @@
                 \expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@}
               \fi
              \fi
-             \ifx\hide@now\n@ 
              \ifx\collect@valtop\yes
              \ifnum\v@lseqtop=\loopcount
                 \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
@@ -13539,14 +14300,11 @@
              \ifnum\v@lseqbbbbottom=\loopcount
                 \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname}
              \fi\fi
-             \fi
              \ifx\collect@restop\yes
              \ifnum\tr@nsseqtop=\loopcount
                 \xdef\last@restop{\last@@restop}
                 \xdef\last@@restop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatetop{\tr@nslatetop\first@}
-                \fi
+                \xdef\tr@nslatetop{\tr@nslatetop\first@}
                 \innerloopcount=\triple@counttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13556,9 +14314,7 @@
              \ifnum\tr@nsseqttop=\loopcount
                 \xdef\last@resttop{\last@@resttop}
                 \xdef\last@@resttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatettop{\tr@nslatettop\first@}
-                \fi
+                \xdef\tr@nslatettop{\tr@nslatettop\first@}
                 \innerloopcount=\triple@countttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13567,10 +14323,8 @@
              \ifx\collect@restttop\yes
              \ifnum\tr@nsseqtttop=\loopcount
                 \xdef\last@restttop{\last@@restttop}
-                \xdef\last@@restttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
-                \fi
+                \last@@restttop{\first@}
+                \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
                 \innerloopcount=\triple@counttttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13580,9 +14334,7 @@
              \ifnum\tr@nsseqttttop=\loopcount
                 \xdef\last@resttttop{\last@@resttttop}
                 \xdef\last@@resttttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
-                \fi
+                \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
                 \innerloopcount=\triple@countttttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13592,9 +14344,7 @@
              \ifnum\tr@nsseqbottom=\loopcount
                  \xdef\last@resbottom{\last@@resbottom}
                  \xdef\last@@resbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
-                 \fi
+                 \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
                  \innerloopcount=\triple@countbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13604,9 +14354,7 @@
              \ifnum\tr@nsseqbbottom=\loopcount
                  \xdef\last@resbbottom{\last@@resbbottom}
                  \xdef\last@@resbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
                  \innerloopcount=\triple@countbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13616,9 +14364,7 @@
              \ifnum\tr@nsseqbbbottom=\loopcount
                  \xdef\last@resbbbottom{\last@@resbbbottom}
                  \xdef\last@@resbbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
                  \innerloopcount=\triple@countbbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13628,9 +14374,7 @@
              \ifnum\tr@nsseqbbbbottom=\loopcount
                  \xdef\last@resbbbbottom{\last@@resbbbbottom}
                  \xdef\last@@resbbbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
                  \innerloopcount=\triple@countbbbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13645,8 +14389,7 @@
           \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{%
                            \the\innerloopcount}
          \else
-          \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi
-          \ifx\hide@now\n@
+          \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
           \ifx\collect@valtop\yes
           \ifnum\v@lseqtop=\loopcount
              \xdef\v@ltop{\v@ltop,N}
@@ -13711,31 +14454,8 @@
           \ifnum\tr@nsseqbbbbottom=\loopcount
               \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -}
           \fi\fi
-          \fi
          \fi
     \ifnum\loopcount<\seq@count \repeat
-       \ifnum\rule@num=0  
-           \ifnum\cons@count=\rule@tens
-              \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
-                 \xdef\temp@{\rule@tens}
-              \else
-                 \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
-              \fi
-              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
-              \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
-              \ifnum\innerloopcount=0 
-                 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
-              \fi
-              \xdef\rule@tens{\the\innerloopcount}
-           \else
-              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
-           \fi 
-           \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
-           \else
-             \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
-           \fi
-       \fi 
-       \ifx\hide@now\n@
          \ifx\collect@cons@graphtop\yes
                 \outerloopcount=1\relax
                 \temp@count=0\relax
@@ -13809,13 +14529,8 @@
                 \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
              \fi
          \fi
-       \fi
 
-%%%%%%%%%%%%%    
-    \ifx\hide@now\y@
-       \regionalshadenowtrue \regionaltintnowtrue
-       \regionalemphnowtrue  \framenowtrue
-    \fi
+    \xdef\g@p{n}
     \ifregionalshadenow \calc@regshade \fi
     \ifregionaltintnow  \calc@regtint  \fi
     \ifregionalemphnow  \calc@regemph  \fi
@@ -13828,17 +14543,6 @@
     \ifbbottomfeaturenow   \xdef\bottop@{bbottom}   \calc@feature \fi
     \ifbbbottomfeaturenow  \xdef\bottop@{bbbottom}  \calc@feature \fi
     \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi
-    \ifx\hide@now\y@
-      \xdef\hidebar@on{1}
-      \ifnum\pos@count=\bar@pos
-      \else
-       \loopcount=\pos@count
-       \advance\loopcount by -\bar@pos
-       \xdef\bar@pos{\the\pos@count}
-       \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;}
-      \fi
-    \else
-%%%%%%%%%%%%%    
     \advance\pos@count by 1 
      \ifshow@logo         \calc@logo     \fi
      \ifall@fshade \all@funcshade
@@ -13854,10 +14558,31 @@
        \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi
       \fi
      \fi
-%%%%%%%%
-    \fi
-    \xdef\hide@now{n}
-%%%%%%%%
+     \ifnum\rule@num=0 
+         \ifx\g@p\y@  
+           \xdef\ruler@{\ruler@ -}
+         \else
+           \ifnum\cons@count=\rule@tens
+              \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+                 \xdef\temp@{\rule@tens}
+              \else
+                 \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+              \fi
+              \xdef\ruler@{\ruler@ !<\temp@>}
+              \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
+              \ifnum\innerloopcount=0 
+                 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+              \fi
+              \xdef\rule@tens{\the\innerloopcount}
+           \else
+              \xdef\ruler@{\ruler@ -}
+           \fi 
+           \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
+           \else
+             \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
+           \fi
+         \fi
+     \fi 
     \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax 
       \c@nsensus 
     \else 
@@ -13900,6 +14625,11 @@
            \ifnum\res@count=0
               \ifx\allow@zero\n@ \advance\res@count by 1 \fi
            \fi
+           \ifx\dom@in\y@ 
+              \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+              \expandafter\get@dom@count\temp@ 
+              \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+           \fi %%%%%%%%%%%*****
            \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
            \ifnum\rule@num=\loopcount
               \temp@count=\csname res@count\the\loopcount\endcsname
@@ -13929,10 +14659,6 @@
                      \csname sequence\the\loopcount\endcsname @}
  \ifnum\loopcount<\seq@count \repeat
  \end@count=0 \count@first \end@count=0 \xdef\start@number{0}
- \ifx\hide@now\n@
-    \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
-    \framenowfalse
- \fi
  \topfeaturenowfalse     \bottomfeaturenowfalse
  \ttopfeaturenowfalse    \bbottomfeaturenowfalse
  \tttopfeaturenowfalse   \bbbottomfeaturenowfalse
@@ -14072,7 +14798,7 @@
 \loop
  \advance\loopcount by 1
     \ifnumbers@left
-       \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax
+       \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax 
        \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
                    \innerloopcount
           \res@count=\innerloopcount
@@ -14083,6 +14809,11 @@
              \ifx\allow@zero\n@ \advance\res@count by 1 \fi
           \fi
        \fi
+       \ifx\dom@in\y@
+            \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+            \expandafter\get@dom@count\temp@
+            \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@}
+       \fi         %%%%%%%%%%*****
        \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
        \ifnames@right
           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
@@ -14092,15 +14823,18 @@
               <\csname newseqname\the\loopcount\endcsname>
               \csname res@count\the\loopcount\endcsname)}
        \fi
-       \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
-                   \innerloopcount
+       \ifx\dom@in\y@
        \else
-          \res@count=\csname res@count\the\loopcount\endcsname
-          \advance\res@count by -1
-          \ifnum\res@count=0
-             \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+          \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
+                      \innerloopcount
+          \else
+             \res@count=\csname res@count\the\loopcount\endcsname
+             \advance\res@count by -1
+             \ifnum\res@count=0
+                \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+             \fi
+	         \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
           \fi
-	      \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
        \fi
     \else
        \ifnames@right
@@ -14110,8 +14844,16 @@
               <\csname newseqname\the\loopcount\endcsname>}
        \fi
     \fi
-    \innerloopcount=\csname res@count\the\loopcount\endcsname
-    \advance\innerloopcount by \res@perline \advance\innerloopcount by 1
+    \ifx\dom@in\y@
+         \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname}
+         \expandafter\get@dom@count\temp@
+         \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@}
+         \innerloopcount=\res@count
+    \else        
+         \innerloopcount=\csname res@count\the\loopcount\endcsname
+         \advance\innerloopcount by \res@perline
+    \fi              %%%%%%%%%%%%%*****
+    \advance\innerloopcount by 1
     \ifregionalshade
          \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
          \else
@@ -14515,6 +15257,7 @@
          \def\res@@style{\csname func@style#1\endcsname}%
          \if\last@ *\def\last@{0}\fi
          \if\last@ /\def\last@{10}\fi
+         \if\last@ !\def\last@{11}\fi
    \else%
    \iffuncmode%
          \xdef\boxc@l@r{\csname fg@color#1\endcsname}%
@@ -14522,8 +15265,9 @@
          \def\res@@style{\csname func@style#1\endcsname}%
          \if\last@ *\def\last@{0}\fi
          \if\last@ /\def\last@{10}\fi
+         \if\last@ !\def\last@{11}\fi
    \else%
-   \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+   \ifcase\last@\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
              \def\res@@style{\all@style}%
          \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
              \def\res@@style{\id@style}%
@@ -14539,7 +15283,9 @@
              \def\res@@style{\csname relax\endcsname}%
          \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
              \def\res@@style{\csname relax\endcsname}%
-         \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+             \def\res@@style{\csname relax\endcsname}%
+         \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
              \def\res@@style{\csname relax\endcsname}%
    \fi\fi\fi\fi%
    \ifx\second@\comm@%
@@ -14581,6 +15327,9 @@
       \if\last@ *%
          \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
       \else%
+      \if\last@ !%
+         \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
+      \else%
       \if\last@ /%
          \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
       \else%
@@ -14605,18 +15354,22 @@
          \else
             \xdef\textc@l@r{\c@nsc@l}%
          \fi%
-      \fi\fi\fi%
+      \fi\fi\fi\fi%
       \def\res@@style{\csname relax\endcsname}%
    \else%
    \ifT@coffee%
       \if\last@ *%
          \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
       \else%
-         \if\last@ /%
-            \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \if\last@ !%
+            \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
          \else%
-            \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
-             \def\res@@style{\csname relax\endcsname}%
+            \if\last@ /%
+               \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+            \else%
+               \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
+               \def\res@@style{\csname relax\endcsname}%
+            \fi
          \fi%
       \fi%
    \else%
@@ -14636,7 +15389,9 @@
              \def\res@@style{\csname relax\endcsname}%
          \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
              \def\res@@style{\csname relax\endcsname}%
-         \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+             \def\res@@style{\csname relax\endcsname}%
+         \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
              \def\res@@style{\csname relax\endcsname}%
    \fi\fi\fi\fi%
    \xdef\first@{#3@}%
@@ -15650,124 +16405,6 @@
    \fi%
    \fi%
 }
-\def\next@hidebar#1;#2;#3;#4@{%
-   \xdef\first@{#1}%
-   \ifx\first@\ampers@nd%
-   \else%
-      \fontfamily{\hideblock@family}\fontseries{\hideblock@series}%
-      \fontshape{\hideblock@shape}%
-      \selectfont%
-      \newline\hbox{}%
-      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
-      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
-      \hbox to -\box@width{\hss}%
-      \kern-0.1\box@width%
-      \xdef\last@{#3[,]&}\expandafter\opt@color\last@%
-      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
-      \textcolor{\f@color}{%
-      \hbox to \first@\box@width{}%
-      \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}%
-      \xdef\last@{#2[,]&}\expandafter\opt@color\last@%
-      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
-      \vspace{-0.23\box@height}%
-      \xdef\temp@{triangle}%
-      \ifx\fourth@\temp@%
-      \else
-      \xdef\temp@{square}%
-      \ifx\fourth@\temp@%
-      \else
-      \xdef\temp@{none}%
-      \ifx\fourth@\temp@%
-      \else
-      \vspace{-0.06\box@height}%
-      \fi\fi\fi%
-      \newline\hbox{}%
-      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
-      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
-      \hbox to -\box@width{\hss}%
-      \hbox to \first@\box@width{}%
-      \kern-0.1\box@width%
-      \textcolor{\f@color}{%
-      \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}%
-      \xdef\first@{triangle}%
-      \ifx\fourth@\first@%
-         \kern-0.582\box@width%
-         \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}%
-         \kern-0.418\box@width%
-      \else
-         \xdef\first@{square}%
-         \ifx\fourth@\first@%
-            \kern-0.6\box@width%
-            \raisebox{-0.12\box@height}{%
-            \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}%
-            \raisebox{-0.19\box@height}{%
-            \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
-            \kern-1.4\box@width%
-         \else
-            \xdef\first@{none}%
-            \ifx\fourth@\first@%
-               \kern-0.6\box@width%
-               \raisebox{-0.19\box@height}{%
-               \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
-               \kern-0.4\box@width%
-            \else
-               \kern-0.6\box@width%
-               \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}%
-               \kern-0.4\box@width%
-            \fi%
-         \fi%
-      \fi%
-      \kern-0.58\box@width%
-      \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}%
-      \xdef\first@{#4@}}%
-   \fi
-}
-\def\put@@hidebar{%
-   \if\first@ @%
-   \else
-      \hbox to -\box@width{\hss}%
-      \expandafter\next@hidebar\first@%
-      \put@@hidebar%
-   \fi%
-}
-\def\put@hidebar{%
-   \ifx\hide@seqs\n@%
-   \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi%
-   \temp@count=\seq@count%
-   \advance\temp@count by 1%
-   \ifx\hide@seqs\y@
-      \advance\temp@count by -1 %
-   \else%
-   \loopcount=1%
-   \xdef\first@{true}%
-   \loop%
-      \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@%
-         \advance\temp@count by -1\fi%
-      \advance\loopcount by 1%
-   \ifnum\loopcount>\seq@count\else\repeat%
-   \fi
-   \ifnum\temp@count>0%
-   \setlength\temp@@length{\box@height}%
-   \advance\temp@@length by \box@depth%
-   \setlength\arrow@height{0.5\temp@@length}%
-   \setlength\temp@@length{\temp@count\temp@@length}%
-   \advance\temp@@length by \arrow@height%
-   \advance\temp@@length by -0.75\box@height%%%%%%%
-   \setlength\arrow@width{\sep@space}%
-   \setlength\arrow@width{\seq@gap@num\arrow@width}%
-   \advance\temp@@length by \arrow@width%
-   \vspace{\arrow@height}%
-   \vspace{-\temp@@length}%
-   \vspace{-2.56\baselineskip}%
-   \xdef\first@{\stylehidebar @}%
-   \put@@hidebar%
-   \vspace{-\arrow@height}%
-   \vspace{-0.47\box@height}%
-   \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi%
-   \newline\hbox{}%
-   \fi%
-   \fi%
-}
 \def\decimal@A#1#2@{%
    \def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}%
    \xdef\temp@@{#1}%
@@ -15899,14 +16536,15 @@
                              \expandafter\decimal@E\fourth@%
       \fi\fi\fi\fi%
       \xdef\fourth@{\fl@g\temp@}%
-      \if\first@ W%
+      \if\first@ W%  
          \hbox to \box@width{\hss%
-         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{0.8}[\third@]%
+         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]%
          {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}%
          \kern-\box@width%
       \else%
-         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{1}[\third@]%
-         {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}%
+         \hbox to \box@width{\hss%
+         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]%
+         {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}%
          \kern-\box@width%
       \fi%
       \advance\temp@count by \second@%
@@ -16205,7 +16843,7 @@
 
 \def\set@lines{%
    \pos@count=1
-   \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}%
+   \xdef\frame@pos{1}\xdef\bar@pos{0}%
    \xdef\featurepostop{1}    \xdef\featureposbottom{1}%
    \xdef\featureposttop{1}   \xdef\featureposbbottom{1}%
    \xdef\featurepostttop{1}  \xdef\featureposbbbottom{1}%
@@ -16327,9 +16965,6 @@
       \ifnum\frame@on=0 \xdef\frame@{0}\fi%
       \put@frame%
    \fi%
-   \ifnum\hidebar@on=1 %
-      \put@hidebar%
-   \fi%
    \ifshow@logo\ifnum\logo@top=1 %
       \xdef\last@{\stack@sequencelogo @}%
       \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi
@@ -16435,7 +17070,7 @@
       \fi
    \fi
    \xdef\consensus{} \xdef\ruler@{}
-   \xdef\styleframe{}         \xdef\stylehidebar{}
+   \xdef\styleframe{}         
    \xdef\textfeaturetop{}     \xdef\textfeaturebottom{}
    \xdef\textfeaturettop{}    \xdef\textfeaturebbottom{}
    \xdef\textfeaturetttop{}   \xdef\textfeaturebbbottom{}
@@ -16559,7 +17194,7 @@
     \xdef\textfeaturebbottom{}   \xdef\featureonbbottom{0}
     \xdef\textfeaturebbbottom{}  \xdef\featureonbbbottom{0}
     \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0}
-    \xdef\styleframe{}        \xdef\stylehidebar{}
+    \xdef\styleframe{} 
     \xdef\stylefeaturetop{}
     \xdef\stylefeaturettop{}
     \xdef\stylefeaturetttop{}
@@ -16570,6 +17205,134 @@
     \xdef\stylefeaturebbbbottom{}}
 \def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
 \def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
+\def\domain@count{%
+    \loopcount=0
+    \ifT@coffee
+       \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+       \expandafter\res@get\seq@line
+       \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+       \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+    \fi
+    \loop
+       \advance\loopcount by 1
+       \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+       \expandafter\res@get\seq@line
+       \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
+       \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+       \ifT@coffee
+          \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+          \expandafter\res@get\seq@line
+          \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+       \fi
+    \ifnum\loopcount<\seq@count\repeat
+    \ifx\first@\ampers@nd
+    \else
+     \ifnum\next@domain@num>-99999\relax
+         \ifnum\domain@seq=0
+             \temp@count=\csname dom@count0\endcsname 
+             \advance\temp@count by 1
+             \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count}
+         \fi
+         \loopcount=0
+         \loop
+           \advance\loopcount by 1
+            \xdef\first@{\csname res\the\loopcount\endcsname}
+            \expandafter\check@char\first@
+            \ifletter
+               \temp@count=\csname dom@count\the\loopcount\endcsname 
+               \advance\temp@count by 1
+               \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count}
+               \if\seq@type A \relax
+                  \temp@count=\char@num
+                  \ifnum\temp@count>96 \advance\temp@count by -32 \fi
+                  \ifnum\temp@count=69 \guess@protein
+                  \else
+                  \ifnum\temp@count=70 \guess@protein
+                  \else
+                  \ifnum\temp@count=73 \guess@protein
+                  \else
+                  \ifnum\temp@count=76 \guess@protein
+                  \else
+                  \ifnum\temp@count=80 \guess@protein
+                  \else
+                  \ifnum\temp@count=81 \guess@protein
+                  \fi\fi\fi\fi\fi\fi
+               \fi
+            \fi
+         \ifnum\loopcount<\seq@count\repeat
+         \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num
+            \advance\total@count by 1
+            \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
+            \loopcount=0
+            \ifx\g@p\y@
+               \ifT@coffee
+                  \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                   \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+               \fi
+            \fi
+            \ifT@coffee
+               \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+            \fi
+            \loop
+               \advance\loopcount by 1
+               \ifx\g@p\y@
+                  \ifT@coffee
+                     \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                      \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+                  \fi
+                  \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+                                   \csname sequence\the\loopcount\endcsname\equ@l}
+                  \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+                                   \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                  \ifnum\outerloopcount=0
+                     \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                      \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                  \fi
+               \fi
+               \ifT@coffee
+                  \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                   \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+               \fi
+               \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+                                \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
+               \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+                                \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+               \ifnum\outerloopcount=0
+                  \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                   \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+               \fi
+            \ifnum\loopcount<\seq@count\repeat
+            \expandafter\get@item\domain@num@list
+            \xdef\domain@num@list{\first@}
+            \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999}
+            \else
+               \loopcount=\next@domain@num
+               \advance\loopcount by 1
+               \ifnum\loopcount=\fourth@
+                  \xdef\g@p{n}
+               \else
+                  \xdef\g@p{y}
+                     \advance\total@count by 1
+                     \advance\outerloopcount by 1
+                     \ifnum\outerloopcount=\res@perline
+                        \outerloopcount=0
+                        \loopcount=0
+                        \loop
+                           \advance\loopcount by 1
+                           \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                            \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                        \ifnum\loopcount<\seq@count\repeat
+                     \fi
+               \fi
+               \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@}
+            \fi
+         \fi 
+         \domain@count
+     \fi
+    \fi
+}
 \def\residue@count{%
     \expandafter\res@get\seq@line
     \if\first@\ampers@nd
@@ -16648,6 +17411,55 @@
          \fi
        \fi
     \ifeof\alignfile
+     \ifx\dom@in\y@
+       \loopcount=0
+       \ifT@coffee
+          \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+          \expandafter\get@temp\temp@
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+       \fi
+       \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+             \expandafter\get@temp\temp@
+             \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+          \fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+          \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \ifnum\loopcount<\seq@count\repeat
+       \xdef\domain@num@list{}
+       \xdef\last@{\stack@dom}
+       \get@domain
+       \xdef\domain@num@list{\domain@num@list &,@}
+       \expandafter\get@item\domain@num@list
+       \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+       \domain@count
+       \loopcount=0
+       \ifT@coffee
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+       \fi
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+          \fi
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                           \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+       \ifnum\loopcount<\seq@count\repeat
+       \if\seq@type A \guess@DNA \fi
+       \advance\seq@pointer by \total@count\relax
+       \xdef\total@pos{\the\total@count}
+    
+     \else   
+
        \ifnum\start@seq=0
           \xdef\seq@line{\csname sequence1\endcsname &@} 
        \else
@@ -16665,9 +17477,10 @@
        \advance\total@count by \first@\relax
        \xdef\first@{\the\total@count}
        \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
-       \ifshow@sublogo \prep@sublogo \fi
-       \ifshow@logo  \prep@logo  \fi
-       \ifnum\seq@pointer>\res@perline \block@output \fi 
+     \fi       
+     \ifshow@sublogo \prep@sublogo \fi
+     \ifshow@logo  \prep@logo  \fi
+     \ifnum\seq@pointer>\res@perline \block@output \fi 
     \else \read@loop
     \fi}
 \def\read@fasta{%
@@ -16697,6 +17510,55 @@
          \fi
        \fi
     \ifeof\alignfile
+     \ifx\dom@in\y@
+       \loopcount=0
+       \ifT@coffee
+          \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+          \expandafter\get@temp\temp@
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+       \fi
+       \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+             \expandafter\get@temp\temp@
+             \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} 
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+          \fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+          \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \ifnum\loopcount<\seq@count\repeat
+       \xdef\domain@num@list{}
+       \xdef\last@{\stack@dom}
+       \get@domain
+       \xdef\domain@num@list{\domain@num@list &,@}
+       \expandafter\get@item\domain@num@list
+       \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+       \domain@count
+       \loopcount=0
+       \ifT@coffee
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+       \fi
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+          \fi
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                           \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+       \ifnum\loopcount<\seq@count\repeat
+       \if\seq@type A \guess@DNA \fi
+       \advance\seq@pointer by \total@count\relax 
+       \xdef\total@pos{\the\total@count}
+    
+     \else   
+    
        \ifnum\start@seq=0
           \xdef\seq@line{\csname sequence1\endcsname &@} 
        \else
@@ -16714,9 +17576,10 @@
        \advance\total@count by \first@\relax
        \xdef\first@{\the\total@count}
        \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
-       \ifshow@sublogo \prep@sublogo \fi
-       \ifshow@logo  \prep@logo  \fi
-       \ifnum\seq@pointer>\res@perline \block@output \fi
+     \fi
+     \ifshow@sublogo \prep@sublogo \fi
+     \ifshow@logo  \prep@logo  \fi
+     \ifnum\seq@pointer>\res@perline \block@output \fi
     \else 
        \read@fasta 
     \fi}
@@ -16847,6 +17710,7 @@
     \fi
     \set@savedseqlength
     \loopcount=0 \xdef\seq@order{}
+    \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
@@ -17280,6 +18144,7 @@
 \xdef\res@numW{0}         \xdef\res@numX{0}
 \xdef\res@numY{0}         \xdef\res@numZ{0}
 \expandafter\xdef\csname res@num\d@t\endcsname{0}
+\expandafter\xdef\csname res@num\equ@l\endcsname{0}
 \xdef\res@corrA{0}        \xdef\res@corrB{0}
 \xdef\res@corrC{0}        \xdef\res@corrD{0}
 \xdef\res@corrE{0}        \xdef\res@corrF{0}
@@ -17294,6 +18159,7 @@
 \xdef\res@corrW{0}        \xdef\res@corrX{0}
 \xdef\res@corrY{0}        \xdef\res@corrZ{0}
 \expandafter\xdef\csname res@corr\d@t\endcsname{0}
+\expandafter\xdef\csname res@corr\equ@l\endcsname{0}
 \xdef\corr@max{0}         \xdef\do@freq@correction{n}
 \xdef\res@total{0}
 \xdef\stack@sequencelogo{} \xdef\bit@total{0}
@@ -17307,12 +18173,11 @@
 \expandafter\xdef\csname group@num1\endcsname{0}
 \expandafter\xdef\csname group@num2\endcsname{0}
 \xdef\exp@rt@num{0}       \xdef\exp@rt{n}
-\xdef\hide@true{n}        \xdef\hide@now{n} 
-\xdef\hide@label{circ}
 \xdef\divref@{0}
 \xdef\all@thresh@ld{100}  \all@shadefalse
 \hidefeaturenames         \hidefeaturestylenames
 \xdef\T@coffee@ccons{n}   \xdef\T@coffee@bcons{n}
+\xdef\dom@in{no}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%                                                                      %%%%%
@@ -17345,6 +18210,8 @@
 \gapchar{.}                         %  . is printed in sequence gaps
 \gaprule{0.3pt}                     %  If a rule is printed in gaps use 0.3 pt
 \gapcolors{Black}{White}            %  Gap symbols appear `Black on White'
+\domaingaprule{1pt}                 %  If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White}        %  Domain separation line appears `Red on White'
 \numberingcolor{Black}              %  Numbering color is `Black'
 \shownumbering{right}               %  Show sequence numbering on the left
 \namescolor{Black}                  %  Names' color is `Black'
@@ -17406,10 +18273,6 @@
 \setseries{featurestyles}{md}       %  Use normal series for feature styles
 \setshape {featurestyles}{up}       %  Use upright shape for feature styles
 \setsize {featurestyles}{normalsize}%  Use normal size for feature styles
-\setfamily{hideblock}{rm}           %  Use roman family for hidden block labels
-\setseries{hideblock}{md}           %  Use normal series for hidden block labels
-\setshape {hideblock}{it}           %  Use italics shape for hidden block labels
-\setsize  {hideblock}{normalsize}   %  Use normal size for hidden block labels
 \setfamily{legend}{tt}              %  Use typewriter family for legend texts
 \setseries{legend}{md}              %  Use normal series for legend texts
 \setshape {legend}{up}              %  Use upright shape for legend texts
@@ -17546,6 +18409,8 @@
 \gapchar{.}                         %  . is printed in sequence gaps
 \gaprule{0.3pt}                     %  If a rule is printed in gaps use 0.3 pt
 \gapcolors{Black}{White}            %  Gap symbols appear `Black on White'
+\domaingaprule{1pt}                 %  If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White}        %  Domain separation line appears `Red on White'
 \numberingcolor{Black}              %  Numbering color is `Black'
 \shownumbering{right}               %  Show sequence numbering on the left
 \namescolor{Black}                  %  Names' color is `Black'
@@ -17603,10 +18468,6 @@
 \setseries{features}{md}            %  Use normal series for feature texts
 \setshape {features}{it}            %  Use italics shape for feature texts
 \setsize  {features}{normalsize}    %  Use normal size for feature texts
-\setfamily{hideblock}{rm}           %  Use roman family for hidden block labels
-\setseries{hideblock}{md}           %  Use normal series for hidden block labels
-\setshape {hideblock}{it}           %  Use italics shape for hidden block labels
-\setsize  {hideblock}{normalsize}   %  Use normal size for hidden block labels
 \setfamily{legend}{tt}              %  Use typewriter family for legend texts
 \setseries{legend}{md}              %  Use normal series for legend texts
 \setshape {legend}{up}              %  Use upright shape for legend texts
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins
index 7f548d9cdb8..51f043c8d20 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.ins
+++ b/Master/texmf-dist/source/latex/texshade/texshade.ins
@@ -1,7 +1,7 @@
 %%
 %% docstrip install file for texshade.sty
 %%
-%% Copyright 1999-2008 Eric Beitz
+%% Copyright 1999-2009 Eric Beitz
 %%
 \def\batchfile{texshade.ins}
 
@@ -14,7 +14,7 @@
 
 LaTeX package for typesetting nucleotide and peptide alignments
 
-Copyright (C) 1999-2007 Eric Beitz
+Copyright (C) 1999-2009 Eric Beitz
 See the file texshade.txt
 
 \endpreamble
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def
index 2de06346a09..a69d64f5d23 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.def
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.def
@@ -32,6 +32,8 @@
 \gapchar{.}                         %  . is printed in sequence gaps
 \gaprule{0.3pt}                     %  If a rule is printed in gaps use 0.3 pt
 \gapcolors{Black}{White}            %  Gap symbols appear `Black on White'
+\domaingaprule{1pt}                 %  If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White}        %  Domain separation line appears `Red on White'
 \numberingcolor{Black}              %  Numbering color is `Black'
 \shownumbering{right}               %  Show sequence numbering on the left
 \namescolor{Black}                  %  Names' color is `Black'
@@ -89,10 +91,6 @@
 \setseries{features}{md}            %  Use normal series for feature texts
 \setshape {features}{it}            %  Use italics shape for feature texts
 \setsize  {features}{normalsize}    %  Use normal size for feature texts
-\setfamily{hideblock}{rm}           %  Use roman family for hidden block labels
-\setseries{hideblock}{md}           %  Use normal series for hidden block labels
-\setshape {hideblock}{it}           %  Use italics shape for hidden block labels
-\setsize  {hideblock}{normalsize}   %  Use normal size for hidden block labels
 \setfamily{legend}{tt}              %  Use typewriter family for legend texts
 \setseries{legend}{md}              %  Use normal series for legend texts
 \setshape {legend}{up}              %  Use upright shape for legend texts
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index a3cd5b24ade..96221a75e00 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -8,13 +8,13 @@
 %% 
 %% LaTeX package for typesetting nucleotide and peptide alignments
 %% 
-%% Copyright (C) 1999-2007 Eric Beitz
+%% Copyright (C) 1999-2009 Eric Beitz
 %% See the file texshade.txt
 %% 
 
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
-\message{Package `texshade', Version 1.17 of 2007/06/19.}
+\ProvidesPackage{texshade}[2009/03/09 LaTeX TeXshade (v1.19)]
+\message{Package `texshade', Version 1.19 of 2009/03/09.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -137,8 +137,10 @@
 \def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&}
 \def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
 \def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
-\def\gap@char{.} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
 \def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
+\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
 \def\fgroup@num{0} \def\max@seqnumber{0}  \def\@lign@count{0}
 \def\resn@m@tch{upper} \def\ressimm@tch{upper}
 \def\resm@tch{upper}   \def\res@llm@tch{upper}
@@ -701,6 +703,8 @@
 \expandafter\xdef\csname cons.Z\endcsname{0}
 \expandafter\xdef\csname cons..\endcsname{0}
 
+\expandafter\xdef\csname cons==\endcsname{0}
+
 \def\c@d@ns{%
 \codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
 \codon{B}{---}
@@ -1452,6 +1456,7 @@
                       \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
                       \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}}
 \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}}
+\def\get@temp#1@{\xdef\temp@{#1}}
 \def\TC@get#1#2@{\xdef\char@num{`#1}
                  \ifnum\char@num=45 \xdef\TC@first@{*}
                  \else
@@ -1596,6 +1601,7 @@
    \ifnum\loopcount<\killseq@count \repeat
    \ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi
    \ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi
+   \ifnum\divref@>0  \xdef\divref@{\csname @rd\divref@\endcsname} \fi
    \loopcount=0
    \loop
       \advance\loopcount by 1
@@ -2086,9 +2092,9 @@
    \xdef\second@{rasmol}
    \ifx\temp@\second@
       \funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up}
-      \funcgroup{Arg, Lys, His}{KR}{Blue}{White}{upper}{up}
-      \funcgroup{Phe, Tyr, Trp}{FY}{MidnightBlue}{White}{upper}{up}
-      \funcgroup{Ala, Gly}{G}{Gray}{White}{upper}{up}
+      \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up}
+      \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up}
+      \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up}
       \funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up}
       \funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up}
       \funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up}
@@ -2154,14 +2160,6 @@
       \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
    \fi\fi
 }
-\def\get@hideregions#1..#2,#3@{%
-   \xdef\hide@true{y}
-   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
-   \xdef\last@{\csname stack@hidereg\seq@\endcsname}
-   \xdef\tmpstack{}
-   \sort@hidestack
-   \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack}
-}
 \def\get@fromemphstack#1;#2;#3;#4@{%
    \xdef\first@{#1} \xdef\second@{#2}
    \xdef\third@{#3} \xdef\last@{#4@}
@@ -2194,6 +2192,40 @@
    \sort@emphstack
    \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
 }
+\def\get@fromdomstack#1;#2;#3@{%
+   \xdef\first@{#1} \xdef\second@{#2}
+   \xdef\last@{#3@}
+}
+\def\sort@domstack{%
+   \expandafter\get@fromdomstack\last@
+   \ifx\first@\ampers@nd
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@}
+   \else
+   \ifnum\st@rt<\second@
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@}
+   \else
+      \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack
+   \fi\fi
+}
+\def\get@domainregions#1..#2,#3@{%
+   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+   \xdef\last@{\stack@dom}
+   \xdef\tmpstack{}
+   \sort@domstack
+   \xdef\stack@dom{\tmpstack}
+}
+\def\get@domain{%
+   \expandafter\get@fromdomstack\last@
+   \ifx\first@\ampers@nd
+   \else
+      \loopcount=\first@
+      \loop
+         \xdef\domain@num@list{\domain@num@list \the\loopcount,}
+         \advance\loopcount by 1
+      \ifnum\loopcount>\second@\else\repeat
+      \get@domain
+   \fi
+}
 \def\getregion@fromtintstack#1{%
    \xdef\temp@{#1}
    \xdef\first@{\csname stack@tintreg\temp@\endcsname}
@@ -2365,6 +2397,132 @@
       \fi%
    \fi%
 }
+
+\def\test@PDB#1:#2,#3,#4,#5,#6@{%
+   \xdef\last@{#1[,]&}\expandafter\opt@color\last@
+   \ifx\f@color\comm@
+      \xdef\PDB@distance{no}
+   \else
+      \xdef\f@color{\f@color .&&@}
+      \expandafter\coord@get\f@color
+      \temp@count=\c@@rd
+      \multiply\temp@count by \temp@count
+      \xdef\PDB@distance{\the\temp@count}
+   \fi
+   \xdef\PDB@hitpos{0}
+   \xdef\PDB@stack{}
+   \xdef\PDB@name{#2}
+   \xdef\PDB@type{point}
+   \ifx\fourth@\PDB@type
+      \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+      \xdef\PDB@refnum@a{\fourth@}
+      \ifx\f@color\C@lpha
+         \xdef\PDB@back@side@a{CA}
+      \else
+         \xdef\PDB@back@side@a{side}
+      \fi
+      \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x}
+      \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+      \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi
+      \load@PDB
+      \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+   \else
+      \xdef\PDB@type{line}
+      \ifx\fourth@\PDB@type
+         \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+         \xdef\PDB@refnum{\fourth@}
+         \ifx\f@color\C@lpha
+            \xdef\PDB@back@side{CA}
+         \else
+            \xdef\PDB@back@side{side}
+         \fi
+         \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+         \ifnum\PDB@refnum<\fourth@
+            \xdef\PDB@refnum@a{\PDB@refnum}
+            \xdef\PDB@refnum@b{\fourth@}
+            \xdef\PDB@back@side@a{\PDB@back@side}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side@b{CA}
+            \else
+               \xdef\PDB@back@side@b{side}
+            \fi
+         \else
+            \xdef\PDB@refnum@b{\PDB@refnum}
+            \xdef\PDB@refnum@a{\fourth@}
+            \xdef\PDB@back@side@b{\PDB@back@side}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side@a{CA}
+            \else
+               \xdef\PDB@back@side@a{side}
+            \fi
+         \fi
+         \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+         \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+         \load@PDB
+         \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+      \else
+         \xdef\PDB@type{plane}
+         \ifx\fourth@\PDB@type
+            \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+            \xdef\PDB@refnum{\fourth@}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side{CA}
+            \else
+               \xdef\PDB@back@side{side}
+            \fi
+            \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+            \ifnum\PDB@refnum<\fourth@
+               \xdef\PDB@refnum@a{\PDB@refnum}
+               \xdef\PDB@refnum@b{\fourth@}
+               \xdef\PDB@back@side@a{\PDB@back@side}
+               \ifx\f@color\C@lpha
+                  \xdef\PDB@back@side@b{CA}
+               \else
+                  \xdef\PDB@back@side@b{side}
+               \fi
+            \else
+               \xdef\PDB@refnum@b{\PDB@refnum}
+               \xdef\PDB@refnum@a{\fourth@}
+               \xdef\PDB@back@side@b{\PDB@back@side}
+               \ifx\f@color\C@lpha
+                  \xdef\PDB@back@side@a{CA}
+               \else
+                  \xdef\PDB@back@side@a{side}
+               \fi
+            \fi
+            \xdef\last@{#5[,]&}\expandafter\opt@color\last@
+            \xdef\PDB@refnum{\fourth@}
+            \ifx\f@color\C@lpha
+               \xdef\PDB@back@side{CA}
+            \else
+               \xdef\PDB@back@side{side}
+            \fi
+            \ifnum\PDB@refnum>\PDB@refnum@b
+               \xdef\PDB@refnum@c{\PDB@refnum}
+               \xdef\PDB@back@side@c{\PDB@back@side}
+            \else
+               \ifnum\PDB@refnum>\PDB@refnum@a
+                  \xdef\PDB@refnum@c{\PDB@refnum@b}
+                  \xdef\PDB@back@side@c{\PDB@back@side@b}
+                  \xdef\PDB@refnum@b{\PDB@refnum}
+                  \xdef\PDB@back@side@b{\PDB@back@side}
+               \else
+                  \xdef\PDB@refnum@c{\PDB@refnum@b}
+                  \xdef\PDB@back@side@c{\PDB@back@side@b}
+                  \xdef\PDB@refnum@b{\PDB@refnum@a}
+                  \xdef\PDB@back@side@b{\PDB@back@side@a}
+                  \xdef\PDB@refnum@a{\PDB@refnum}
+                  \xdef\PDB@back@side@a{\PDB@back@side}
+               \fi
+            \fi
+            \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+            \load@PDB
+            \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+         \fi
+      \fi
+   \fi
+}
+
 \def\test@fill#1:#2:#3&{%
    \xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@%
    \xdef\second@@{\fourth@}%
@@ -2541,6 +2699,7 @@
     \expandafter\xdef\csname \prfx grpZ\endcsname{-26}
     \expandafter\xdef\csname \prfx grp-\endcsname{-999}
     \expandafter\xdef\csname \prfx grp.\endcsname{-999}
+    \expandafter\xdef\csname \prfx grp=\endcsname{-999}
 }
 \def\inactivate@chars{%
    \catcode`\#=12
@@ -2555,9 +2714,15 @@
 \def\romancount{\@roman\loopcount}
 \def\Romancount{\@Roman\loopcount}
 \def\cut@name#1.#2@{\global\xdef\file@n@me{#1}}
+\def\coord@get#1.#2#3@{%
+   \xdef\temp@{#2}
+   \ifx\temp@\ampers@nd \xdef\temp@{0} \fi
+   \xdef\c@@rd{#1\temp@}
+}
 \def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{%
     \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3}  \xdef\fourth@{#4}
-    \xdef\fifth@{#5} \xdef\sixth@{#6}  \xdef\seventh@{#7}\xdef\eighth@{#8}}
+    \xdef\fifth@{#5} \xdef\sixth@{#6}  \xdef\seventh@{#7}\xdef\eighth@{#8}
+    \xdef\nineth@{#9}}
 \def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}}
 \def\write@PHDsec{%
  \expandafter\get@sim\last@
@@ -3525,7 +3690,7 @@
   \xdef\fourth@{#2,&,@}
   \expandafter\get@triplet\fourth@
    \fi}
-
+\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}}
 \def\get@name@number{%
    \xdef\second@{n}
    \loopcount=0
@@ -3542,6 +3707,318 @@
    \fi
 }
 
+\def\calc@distance@point{%
+   \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax
+   \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+   \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax
+   \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+   \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax
+   \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+   \advance\loopcount by \y@distance\relax
+   \advance\loopcount by \x@distance\relax
+   \ifnum\loopcount > \PDB@distance \else
+      \loopcount=\PDB@hitpos \advance\loopcount by 1
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
+\def\calc@distance@line{%
+   \loopcount=\x@coord\relax \multiply\loopcount by \x@orient
+   \temp@count=\y@coord \relax \multiply\temp@count by \y@orient
+   \advance\loopcount by \temp@count
+   \temp@count=\z@coord \relax \multiply\temp@count by \z@orient
+   \advance\loopcount by \temp@count
+   \advance\loopcount by -\c@nst@
+   \xdef\z@hler{\the\loopcount}
+   \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a
+   \advance\loopcount by -\x@coord
+   \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+   \loopcount=\z@hler
+   \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a
+   \advance\loopcount by -\y@coord
+   \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+   \loopcount=\z@hler
+   \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a
+   \advance\loopcount by -\z@coord
+   \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+   \advance\loopcount by \y@distance\relax
+   \advance\loopcount by \x@distance\relax
+   \ifnum\loopcount > \PDB@distance \else
+      \loopcount=\PDB@hitpos \advance\loopcount by 1
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
+\def\intr@@t{%
+   \loopcount=\r@@t
+   \temp@count=1
+   \loop
+      \advance\loopcount by \temp@count
+      \divide\loopcount by 2
+      \temp@count=\r@@t
+      \divide\temp@count by \loopcount
+   \ifnum\loopcount>\temp@count\repeat
+}
+
+\def\calc@distance@plane{%
+   \loopcount=\x@coord\relax
+   \multiply\loopcount by \x@orient
+   \temp@count=\y@coord \relax
+   \multiply\temp@count by \y@orient
+   \advance\loopcount by \temp@count
+   \temp@count=\z@coord \relax
+   \multiply\temp@count by \z@orient
+   \advance\loopcount by \temp@count
+   \advance\loopcount by \c@nst@
+   \divide\loopcount by \f@ct@r
+   \multiply\loopcount by \loopcount
+   \ifnum\loopcount > \PDB@distance \else
+      \loopcount=\PDB@hitpos \advance\loopcount by 1
+      \ifnum\loopcount=\PDB@pos
+      \else
+         \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+      \fi
+      \xdef\PDB@hitpos{\PDB@pos}
+   \fi
+}
+
+\def\load@PDB{%
+    \bgroup
+    \immediate\openin\structurefile = \PDB@name\relax
+    \ifeof\structurefile
+      \PackageError{TeXshade}
+      {File `\PDB@name' not found}
+      {\MessageBreak
+       The file you specified is missing or you have \MessageBreak
+       misspelled it. \MessageBreak\MessageBreak
+       No PDB domain labeling will be displayed. \MessageBreak
+       Type <return> to proceed. \MessageBreak
+       Type X <return> to quit. \MessageBreak
+}
+       \immediate\closein\structurefile\egroup
+    \else
+    \message{<reading PDB: \PDB@name>}
+    \xdef\first@{}
+    \loop
+       \read\structurefile to \readline
+       \xdef\test@{\expandafter\string\readline}
+       \ifx\test@\par@
+       \else
+          \xdef\structureline{\readline & & & & & & & & &@}
+          \expandafter\struc@get\structureline
+          \ifx\first@\@TOM
+             \ifx\PDB@back@side@a\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@a
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@a
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@a
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@a
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+                   \fi
+                \fi
+             \fi
+             \ifx\PDB@back@side@b\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@b
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@b
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@b
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@b
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+                   \fi
+                \fi
+             \fi
+             \ifx\PDB@back@side@c\C@lpha
+                \ifx\third@\C@lpha
+                   \xdef\temp@@@{\fifth@ &&@}
+                   \expandafter\check@letter\temp@@@
+                   \ifnumber
+                      \ifnum\fifth@=\PDB@refnum@c
+                         \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+                      \fi
+                   \else
+                      \ifnum\sixth@=\PDB@refnum@c
+                         \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+                         \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+                         \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+                      \fi
+                   \fi
+                \fi
+             \else
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                   \ifnum\fifth@=\PDB@refnum@c
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+                   \fi
+                \else
+                   \ifnum\sixth@=\PDB@refnum@c
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+                   \fi
+                \fi
+             \fi
+          \fi
+       \fi
+    \ifeof\structurefile \else\repeat
+    \closein\structurefile
+    \ifx\PDB@type\@line@
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount}
+       \loopcount=\xref@coord@a \multiply\loopcount by \x@orient
+       \temp@count=\yref@coord@a \multiply\temp@count by \y@orient
+       \advance\loopcount by \temp@count
+       \temp@count=\zref@coord@a \multiply\temp@count by \z@orient
+       \advance\loopcount by \temp@count
+       \xdef\c@nst@{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \x@orient
+       \temp@count=\y@orient \multiply\temp@count by \y@orient
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \z@orient
+       \advance\loopcount by \temp@count
+       \xdef\f@ct@r{\the\loopcount}
+    \fi
+    \ifx\PDB@type\@plane@
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount}
+       \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount}
+       \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount}
+       \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount}
+       \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s
+       \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount}
+       \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s
+       \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount}
+       \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s
+       \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s
+       \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \xref@coord@a
+       \temp@count=\y@orient \multiply\temp@count by \yref@coord@a
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \zref@coord@a
+       \advance\loopcount by \temp@count
+       \multiply\loopcount by -1\relax
+       \xdef\c@nst@{\the\loopcount}
+       \loopcount=\x@orient \multiply\loopcount by \loopcount
+       \temp@count=\y@orient \multiply\temp@count by \temp@count
+       \advance\loopcount by \temp@count
+       \temp@count=\z@orient \multiply\temp@count by \temp@count
+       \advance\loopcount by \temp@count
+       \xdef\r@@t{\the\loopcount} \intr@@t
+       \xdef\f@ct@r{\the\loopcount}
+    \fi
+    \immediate\openin\structurefile = \PDB@name\relax
+    \xdef\first@{}
+    \loop
+       \read\structurefile to \readline
+       \xdef\test@{\expandafter\string\readline}
+       \ifx\test@\par@
+       \else
+          \xdef\structureline{\readline & & & & & & & & &@}
+          \expandafter\struc@get\structureline
+          \ifx\first@\@TOM
+                \xdef\temp@@@{\fifth@ &&@}
+                \expandafter\check@letter\temp@@@
+                \ifnumber
+                      \xdef\PDB@pos{\fifth@}
+                      \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd}
+                \else
+                      \xdef\PDB@pos{\sixth@}
+                      \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd}
+                      \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd}
+                      \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd}
+                \fi
+                \ifnum\PDB@hitpos=\PDB@pos
+                \else
+                   \ifx\PDB@type\@point@
+                      \calc@distance@point
+                   \else
+                      \ifx\PDB@type\@line@
+                         \calc@distance@line
+                      \else
+                         \ifx\PDB@type\@plane@
+                            \calc@distance@plane
+                         \fi
+                      \fi
+                   \fi
+                \fi
+          \fi
+       \fi
+    \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@}
+    \else\repeat
+    \closein\structurefile
+
+   \fi
+   \egroup
+ }
+
 %%%%% Definition of user commands
 
 \def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}}
@@ -3630,6 +4107,34 @@
       \separationline{\the\loopcount}
    \ifnum\loopcount<\seq@count\repeat
    \fi}
+\def\printPDBlist#1{%
+     \xdef\list@{}
+     \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+     \xdef\first@{\list@ &}
+     \ifx\first@\ampers@nd
+     \else
+        \xdef\first@{\list@ @}
+        \loop
+           \expandafter\get@item\first@
+           \fourth@
+        \ifx\first@@\ampers@nd\else{,\ }\repeat
+     \fi
+}
+\def\messagePDBlist#1{%
+     \xdef\list@{}
+     \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+     \xdef\first@{\list@ &}
+     \ifx\first@\ampers@nd
+     \else
+        \message{(#1:}
+        \xdef\first@{\list@ @}%
+        \loop%
+           \expandafter\get@item\first@%
+           \message{\fourth@}%
+        \ifx\first@@\ampers@nd\else\repeat%
+        \message{)}
+     \fi
+}
 \def\shaderegion#1#2#3#4{%
    \regionalshadetrue
    \xdef\seq@{#1}
@@ -3647,6 +4152,7 @@
      \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
      \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@regions\list@
@@ -3670,6 +4176,7 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@tintregions\list@
@@ -3710,6 +4217,7 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@emphregions\list@
@@ -3734,29 +4242,13 @@
    \else
      \xdef\@ll{#3}
      \xdef\list@{#2,&}
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
      \loop
         \xdef\list@{\list@ @}
         \expandafter\get@frameregions\list@
      \ifx\list@\ampers@nd\else\repeat
    \fi
 }
-\def\hideblock#1#2#3#4{%
-   \xdef\seq@{#1}
-   \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
-   \xdef\first@{\seq@ @} \expandafter\check@letter\first@
-   \xdef\first@{\seq@}
-   \ifletter \get@name@number \xdef\seq@{\first@} \fi
-   \ifnum\seq@>\seq@count
-     \message{<Ignored seq `\seq@' in \noexpand\hideblock>}
-   \else
-     \xdef\@ll{#3} \xdef\text@{#4}
-     \xdef\list@{#2,&}
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@hideregions\list@
-     \ifx\list@\ampers@nd\else\repeat
-   \fi
-}
 \def\bargraphstretch#1{\def\b@r@stretch{#1}}
 \def\colorscalestretch#1{\def\sc@le@stretch{#1}}
 \def\rm@@measure#1#2@{%
@@ -4118,7 +4610,7 @@
    \ifx\second@@\last@
       \xdef\list@{#3,&}
       \xdef\style@{#4}
-      \xdef\f@text@{#5}
+      \def\f@text@{#5}
       \do@bargraph
       \xdef\temp@{bottom}
       \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi
@@ -4133,11 +4625,14 @@
    \ifx\second@@\last@
       \xdef\list@{#3,&}
       \xdef\style@{#4}
-      \xdef\f@text@{#5}
+      \def\f@text@{#5}
       \do@colorgraph
    \else
-   \xdef\f@text@{#5}
+   \xdef\f@@color{\f@color}
    \xdef\list@{#3,&}
+   \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
+   \def\f@text@{#5}
+   \xdef\f@color{\f@@color}
    \xdef\temp@{#4&}
    \ifx\temp@\ampers@nd
       \xdef\style@{&}
@@ -4215,7 +4710,9 @@
       \fi
       \fi
    \fi
+   \loopcount=0
    \loop
+      \advance\loopcount by 1\relax
       \xdef\list@{\list@ @}
       \expandafter\get@fregions\list@
    \ifx\list@\ampers@nd\else\repeat
@@ -4273,7 +4770,23 @@
    \def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next}
    \futurelet\l@@k\decide@}
 \def\numberingwidth#1{\def\num@width{#1}}
-\def\charstretch#1{\def\char@stretch{#1}}
+\def\charstretch#1{%
+   \def\char@stretch{#1}
+   \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd
+   \multiply \loopcount by 7
+   \divide \loopcount by 10
+   \ifnum\loopcount<10
+      \xdef\temp@{0\the\loopcount @}
+   \else
+      \xdef\temp@{\the\loopcount @}
+   \fi
+   \expandafter\decimal@B\temp@
+   \ifnum\loopcount>99
+      \xdef\char@stretch@W{#1}
+   \else
+      \xdef\char@stretch@W{\temp@}
+   \fi
+}
 \def\linestretch#1{\def\line@stretch{#1}}
 \def\logostretch#1{%
    \def\logo@stretch{#1}
@@ -4405,6 +4918,7 @@
    \ifx\first@\second@\def\gap@char{o}
    \else\def\gap@char{#1}\fi}
 \def\gaprule#1{\def\gap@rulethick{#1}}
+\def\domaingaprule#1{\def\domgap@rulethick{#1}}
 \newcommand{\setends}[3][&]{%
   \xdef\start@seq{#2}
   \xdef\temp@{consensus}
@@ -4877,9 +5391,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@family{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@family{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@family{\third@}
    \else
@@ -4897,9 +5408,8 @@
       \xdef\residues@family{\third@}
       \xdef\legend@family{\third@}
       \xdef\label@family{\third@}
-      \xdef\hideblock@family{\third@}
       \xdef\ruler@family{\second@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setseries#1#2{%
@@ -4942,9 +5452,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@series{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@series{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@series{\third@}
    \else
@@ -4958,9 +5465,8 @@
       \xdef\namestext@series{\third@}
       \xdef\residues@series{\third@}
       \xdef\legend@series{\third@}
-      \xdef\hideblock@series{\third@}
       \xdef\label@series{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setshape#1#2{%
@@ -5011,9 +5517,6 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@shape{\third@}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@ \xdef\hideblock@shape{\third@}
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@shape{\third@}
    \else
@@ -5027,9 +5530,8 @@
       \xdef\namestext@shape{\third@}
       \xdef\residues@shape{\third@}
       \xdef\legend@shape{\third@}
-      \xdef\hideblock@shape{\third@}
       \xdef\label@shape{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setsize#1#2{%
@@ -5065,20 +5567,6 @@
    \ifx\first@\temp@
       \def\legend@size{\csname #2\endcsname}
    \else
-   \xdef\temp@{hideblock}
-   \ifx\first@\temp@
-      \xdef\temp@@{#2}
-      \xdef\temp@{huge}
-      \ifx\temp@\temp@@
-         \def\hideblock@size{\csname LARGE\endcsname}
-      \else
-      \xdef\temp@{Huge}
-      \ifx\temp@\temp@@
-         \def\hideblock@size{\csname LARGE\endcsname}
-      \else
-         \def\hideblock@size{\csname #2\endcsname}
-      \fi\fi
-   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@
       \def\label@size{\csname #2\endcsname}
@@ -5097,11 +5585,10 @@
       \def\numbertext@size{\csname #2\endcsname}
       \def\namestext@size{\csname #2\endcsname}
       \def\legend@size{\csname #2\endcsname}
-      \def\hideblock@size{\csname #2\endcsname}
       \def\label@size{\csname #2\endcsname}
       \def\residues@size{\csname #2\endcsname}
       \xdef\res@size{#2}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \xdef\temp@{Huge}
    \ifx\temp@\res@size
       \def\bottomruler@size{\csname Large\endcsname}
@@ -5285,25 +5772,6 @@
 \def\legendLARGE       {\setsize{legend}{LARGE}}
 \def\legendhuge        {\setsize{legend}{huge}}
 \def\legendHuge        {\setsize{legend}{Huge}}
-\def\hideblockrm{\setfamily{hideblock}{rm}}
-\def\hideblocksf{\setfamily{hideblock}{sf}}
-\def\hideblocktt{\setfamily{hideblock}{tt}}
-\def\hideblockmd{\setseries{hideblock}{md}}
-\def\hideblockbf{\setseries{hideblock}{bf}}
-\def\hideblockup{\setshape {hideblock}{up}}
-\def\hideblockit{\setshape {hideblock}{it}}
-\def\hideblocksl{\setshape {hideblock}{sl}}
-\def\hideblocksc{\setshape {hideblock}{sc}}
-\def\hideblocktiny        {\setsize{hideblock}{tiny}}
-\def\hideblockscriptsize  {\setsize{hideblock}{scriptsize}}
-\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}}
-\def\hideblocksmall       {\setsize{hideblock}{small}}
-\def\hideblocknormalsize  {\setsize{hideblock}{normalsize}}
-\def\hideblocklarge       {\setsize{hideblock}{large}}
-\def\hideblockLarge       {\setsize{hideblock}{Large}}
-\def\hideblockLARGE       {\setsize{hideblock}{LARGE}}
-\def\hideblockhuge        {\setsize{hideblock}{LARGE}}
-\def\hideblockHuge        {\setsize{hideblock}{LARGE}}
 \def\rulerrm{\setfamily{ruler}{rm}}
 \def\rulersf{\setfamily{ruler}{sf}}
 \def\rulertt{\setfamily{ruler}{tt}}
@@ -5396,6 +5864,12 @@
                                 \expandafter\def\csname fg@textcolor*\endcsname{#1}\fi
                              \ifx\second@\last@\else\def\gap@bg{#2}
                                 \expandafter\def\csname fg@color*\endcsname{#2}\fi}
+\def\domaingapcolors#1#2     {\xdef\first@{#1&}\xdef\second@{#2&}
+                             \xdef\last@{\ampers@nd}
+                             \ifx\first@\last@\else\def\domgap@fg{#1}
+                                \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi
+                             \ifx\second@\last@\else\def\domgap@bg{#2}
+                                \expandafter\def\csname fg@color!\endcsname{#2}\fi}
 \def\shadebox#1{%
    \xdef\first@{White}%
    \xdef\third@{#1}%
@@ -5868,6 +6342,24 @@
    \fi
 }
 
+\def\setdomain#1#2{%
+   \xdef\first@{#1}
+   \xdef\temp@{consensus}
+   \ifx\first@\temp@ \xdef\domain@seq{0}
+   \else
+      \xdef\first@{#1 @} \expandafter\check@letter\first@
+      \xdef\first@{#1}   \ifletter \get@name@number \fi
+      \xdef\domain@seq{\csname @rd\first@\endcsname}%
+   \fi
+   \xdef\list@{#2,&}
+   \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+   \loop
+        \xdef\list@{\list@ @}
+        \expandafter\get@domainregions\list@
+   \ifx\list@\ampers@nd\else\repeat
+   \xdef\dom@in{y}
+}
+
 %%%%%  Calculate consensus
 
 \def\check@sim{%
@@ -5933,7 +6425,6 @@
    \fi
  \else
     \newresfalse
-    \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t}
  \fi
 
  \ifnewres
@@ -6027,13 +6518,29 @@
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
                 \csname seq\the\loopcount\endcsname3\gap@char}
             \else
+             \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l
+              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                 \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y}
+             \else
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
                 \csname seq\the\loopcount\endcsname%
                 3\csname res\the\loopcount\endcsname}
              \fi
+             \fi
           \else
            \xdef\first@{\csname res\the\loopcount\endcsname}
-           \ifx\first@\d@t
+           \ifx\first@\equ@l
+             \def\first@{\dom@char} \def\third@{9}
+             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+             \xdef\first@{=\first@}\fi
+             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+             \xdef\first@{,\first@}\fi
+             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                              \csname seq\the\loopcount\endcsname\third@\first@} \xdef\g@p{y}
+           \else
+             \ifx\first@\d@t
                  \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                       <\csname seq@start\the\loopcount\endcsname
                     \ifsh@wg@ps
@@ -6053,27 +6560,28 @@
                     \fi
                     \fi
                  \fi
-             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
-                \xdef\first@{=\first@}\fi
-             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
-                \xdef\first@{,\first@}\fi
-             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname\third@\first@}
-           \else
-             \ifnum\divref@=\loopcount\else
-             \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
-             \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-             \else \xdef\first@{\resn@m@tch} \fi\fi\fi
-             \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
-             \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
-                \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
                 \xdef\first@{,\first@}\fi
-             \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname3\first@}
+                \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                                 \csname seq\the\loopcount\endcsname\third@\first@}
+             \else
+               \ifnum\divref@=\loopcount\else
+               \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
+               \xdef\low@up{upper} \ifx\resn@m@tch\low@up
+               \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+               \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                  \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                  \xdef\first@{=\first@}\fi
+               \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                  \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                  \xdef\first@{,\first@}\fi
+               \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+                  \csname seq\the\loopcount\endcsname3\first@}
+             \fi
            \fi
           \fi
        \ifnum\loopcount<\seq@count \repeat
@@ -6086,9 +6594,13 @@
        \expandafter\ifx\csname emph@seq0\endcsname\y@
           \expandafter\xdef\csname emph@seq0\endcsname{n}
           \xdef\first@{,\first@}\fi
-       \xdef\consensus{\consensus 4\first@}
-       \expandafter\ifx\csname res\cons@num\endcsname\d@t
+       \ifx\g@p\y@
+          \xdef\consensus{\consensus 8{}}
+       \else
+          \xdef\consensus{\consensus 4\first@}
+          \expandafter\ifx\csname res\cons@num\endcsname\d@t
           \else\xdef\constopo{\constopo 0}\fi
+       \fi
     \else
      \ifnum\cons@num>0
        \xdef\tmp@{\csname res\cons@num\endcsname}
@@ -6104,6 +6616,7 @@
         \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -6111,8 +6624,7 @@
                 \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
                 \xdef\first@{,\first@}\fi
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
-                \csname seq\the\loopcount\endcsname%
-                3\first@}
+                \csname seq\the\loopcount\endcsname3\first@}
         \else
           \xdef\first@{\csname res\the\loopcount\endcsname}
           \xdef\last@{\csname res\the\loopcount\endcsname}
@@ -6123,6 +6635,9 @@
               \xdef\low@up{upper} \ifx\ressimm@tch\low@up
               \else \xdef\first@{\ressimm@tch} \fi\fi\fi
           \else
+            \ifx\first@\equ@l
+              \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y}
+            \else
               \ifx\first@\d@t
                  \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                       <\csname seq@start\the\loopcount\endcsname
@@ -6150,6 +6665,7 @@
                  \xdef\low@up{upper} \ifx\resn@m@tch\low@up
                  \else \xdef\first@{\resn@m@tch} \fi\fi\fi
               \fi
+            \fi
           \fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -6171,8 +6687,12 @@
      \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
-     \xdef\consensus{\consensus5\first@}
-     \xdef\constopo{\constopo 1}
+     \ifx\g@p\y@
+        \xdef\consensus{\consensus 8{}}
+     \else
+        \xdef\consensus{\consensus5\first@}
+        \xdef\constopo{\constopo 1}
+     \fi
     \fi
  \else
  \iffuncmode
@@ -6180,6 +6700,17 @@
     \loop
        \advance\loopcount by 1
        \xdef\first@{\csname res\the\loopcount\endcsname}
+       \ifx\first@\equ@l
+          \def\first@{\dom@char} \def\third@{!}  \xdef\g@p{y}
+          \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{=\first@}\fi
+          \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{,\first@}\fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+             \csname seq\the\loopcount\endcsname\third@\first@}
+       \else
        \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6221,6 +6752,7 @@
           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
              \csname seq\the\loopcount\endcsname0\first@}
        \fi
+       \fi
     \ifnum\loopcount<\seq@count \repeat
  \else
     \loopcount=0
@@ -6230,6 +6762,7 @@
         \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char}  \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -6241,6 +6774,17 @@
                 3\first@}
         \else
          \xdef\first@{\csname res\the\loopcount\endcsname}
+         \ifx\first@\equ@l
+            \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y}
+           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{=\first@}\fi
+           \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{,\first@}\fi
+           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+              \csname seq\the\loopcount\endcsname\third@\first@}
+         \else
          \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6283,6 +6827,7 @@
            \expandafter\xdef\csname seq\the\loopcount\endcsname{%
              \csname seq\the\loopcount\endcsname3\first@}
          \fi
+         \fi
         \fi
     \ifnum\loopcount<\seq@count \repeat
     \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
@@ -6294,8 +6839,12 @@
     \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
-    \xdef\consensus{\consensus 4\first@}
-    \xdef\constopo{\constopo 0}
+    \ifx\g@p\y@
+       \xdef\consensus{\consensus 8{}}
+    \else
+       \xdef\consensus{\consensus 4\first@}
+       \xdef\constopo{\constopo 0}
+    \fi
  \fi\fi}
 
 \def\c@nserved{%
@@ -6307,6 +6856,7 @@
     \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -6345,6 +6895,7 @@
     \xdef\low@up{upper} \ifx\resn@m@tch\low@up
     \else \xdef\first@{\resn@m@tch} \fi\fi\fi
     \fi
+    \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y} \fi
     \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6386,8 +6937,12 @@
  \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 5\first@}
- \xdef\constopo{\constopo 2}}
+ \ifx\g@p\y@
+    \xdef\consensus{\consensus 8{}}
+ \else
+    \xdef\consensus{\consensus 5\first@}
+    \xdef\constopo{\constopo 2}
+ \fi}
 
 \def\allm@tch{%
  \xdef\tmp@{\csname res\cons@seq\endcsname}
@@ -6398,6 +6953,7 @@
     \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
              \xdef\first@{\csname res\the\loopcount\endcsname}
              \ifx\first@\d@t\def\first@{\gap@char}\fi
+             \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -6441,6 +6997,7 @@
     \xdef\low@up{upper} \ifx\resn@m@tch\low@up
     \else \xdef\first@{\resn@m@tch} \fi\fi\fi
     \fi
+    \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y} \fi
     \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6482,8 +7039,12 @@
  \expandafter\ifx\csname emph@seq0\endcsname\y@
                 \expandafter\xdef\csname emph@seq0\endcsname{n}
                 \xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 6\first@}
- \xdef\constopo{\constopo 3}}
+ \ifx\g@p\y@
+    \xdef\consensus{\consensus 8{}}
+ \else
+    \xdef\consensus{\consensus 6\first@}
+    \xdef\constopo{\constopo 3}
+ \fi}
 
 \def\functi@nal{%
      \ifnum\cons@num>0
@@ -6509,6 +7070,9 @@
                 0\first@}
         \else
         \xdef\first@{\csname res\the\loopcount\endcsname}
+         \ifx\first@\equ@l
+            \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+         \else
          \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6540,6 +7104,7 @@
               \xdef\low@up{upper} \ifx\resn@m@tch\low@up
               \else \xdef\first@{\resn@m@tch} \fi\fi
          \fi
+         \fi
         \fi
         \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -6559,6 +7124,7 @@
      \xdef\first@{\csname res\the\loopcount\endcsname}
      \xdef\second@{\csname funcgrp\first@\endcsname}
      \ifnum\second@<0 \xdef\second@{0} \fi
+     \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!}  \xdef\g@p{y} \fi
      \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6609,19 +7175,11 @@
 
 \def\T@coffee@shade{%
    \loopcount=0
-   \expandafter\ifx\csname tint@seq0\endcsname\y@
-                \expandafter\xdef\csname tint@seq0\endcsname{n}
-                \xdef\first@{=\first@}\fi
-   \expandafter\ifx\csname emph@seq0\endcsname\y@
-                \expandafter\xdef\csname emph@seq0\endcsname{n}
-                \xdef\first@{,\first@}\fi
-   \xdef\second@{\csname TC@num0\endcsname}
-   \xdef\consensus{\consensus\second@\n@m@tch}
-   \xdef\constopo{\constopo\second@}
    \loop
      \advance\loopcount by 1
      \xdef\first@{\csname res\the\loopcount\endcsname}
      \xdef\second@{\csname TC@num\the\loopcount\endcsname}
+     \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!}  \xdef\g@p{y} \fi
      \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
                  <\csname seq@start\the\loopcount\endcsname
@@ -6665,7 +7223,22 @@
                 \csname seq\the\loopcount\endcsname%
                 \second@\first@}
      \fi
-   \ifnum\loopcount<\seq@count \repeat}
+   \ifnum\loopcount<\seq@count \repeat
+   \xdef\first@{\csname res0\endcsname}
+   \expandafter\ifx\csname tint@seq0\endcsname\y@
+                \expandafter\xdef\csname tint@seq0\endcsname{n}
+                \xdef\first@{=\first@}\fi
+   \expandafter\ifx\csname emph@seq0\endcsname\y@
+                \expandafter\xdef\csname emph@seq0\endcsname{n}
+                \xdef\first@{,\first@}\fi
+   \xdef\second@{\csname TC@num0\endcsname}
+   \ifx\g@p\y@
+      \xdef\consensus{\consensus 8{}}
+   \else
+      \xdef\consensus{\consensus\second@\n@m@tch}
+      \xdef\constopo{\constopo\second@}
+   \fi
+   }
 
 \def\getregion@fromstack@first{%
       \expandafter\getregion@fromstack{\the\loopcount}
@@ -6708,7 +7281,6 @@
             \fi
          \fi\fi
       \ifnum\loopcount<\seq@count \repeat
-      \ifx\hide@now\n@
       \loopcount=0
       \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@
       \else
@@ -6728,7 +7300,6 @@
                               &\csname shade@style\the\loopcount\endcsname)}
          \fi
       \ifnum\loopcount<\seq@count \repeat
-      \fi
 }
 
 \def\getregion@fromemphstack@first{%
@@ -7089,13 +7660,13 @@
          \xdef\cons@val{\csname TC@num0\endcsname}
          \if\cons@val *
             \xdef\cons@val{99}
-         \fi   \message{(b(\cons@val)b)}
+         \fi
       \fi
       \ifx\T@coffee@ccons\y@
          \xdef\cons@val{\csname TC@num0\endcsname}
          \if\cons@val *
             \xdef\cons@val{99}
-         \fi   \message{(c(\cons@val)c)}
+         \fi
       \fi
    \fi
 }
@@ -7990,11 +8561,24 @@
       \ifnum\loopcount<\seq@count \repeat
 }
 
+\def\add@to@rule@tens{%
+    \advance\innerloopcount by \ruler@step\relax
+    \ifnum\innerloopcount=0
+          \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+    \fi
+    \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens
+    \else
+       \xdef\rule@tens{\the\innerloopcount}
+    \fi
+}
+
 \def\c@nsensus{%
  \ifnum\pos@count>\res@perline
     \else
     \loopcount=0
-    \global\advance\cons@count by 1\relax
+    \ifx\g@p\n@
+       \global\advance\cons@count by 1\relax
+    \fi
     \ifnum\cons@count=0\relax
        \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
     \fi
@@ -8003,21 +8587,6 @@
             \expandafter\TC@get\TC@line
     \fi
     \expandafter\xdef\csname res@count0\endcsname{\the\cons@count}
-    \ifx\hide@true\y@
-    \expandafter\ifx\csname hidestart0\endcsname\ampers@nd
-    \else
-       \expandafter\ifnum\csname hidestart0\endcsname>\cons@count
-       \else
-          \expandafter\ifnum\csname hidestop0\endcsname<\cons@count
-          \else
-             \xdef\hide@now{y} \xdef\eighth@{0}
-          \fi
-          \expandafter\ifnum\csname hidestop0\endcsname=\cons@count
-             \getregion@fromhidestack{0}
-          \fi
-    \fi
-    \fi
-    \fi
     \loop
          \advance\loopcount by 1
          \ifT@coffee
@@ -8032,46 +8601,35 @@
          \advance\innerloopcount by 1
          \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount}
          \expandafter\check@char\first@
+         \ifx\dom@in\y@ %%%%%%%%%%%*****
+                \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+                \expandafter\get@dom@count\temp@
+                \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+         \fi            %%%%%%%%%%%*****
          \ifletter
-             \res@count=\csname res@count\the\loopcount\endcsname
-             \advance\res@count by 1
-             \ifnum\res@count=0\relax
-                \ifx\allow@zero\n@ \advance\res@count by 1 \fi
-             \fi
-             \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
-             \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
-             \ifx\hide@true\y@
-             \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd
-             \else
-             \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count
+             \ifx\dom@in\y@
              \else
-                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count
-                \else
-                   \xdef\hide@now{y}\xdef\eighth@{\the\loopcount}
-                \fi
-                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count
-                   \xdef\first@@{\first@}
-                   \expandafter\getregion@fromhidestack{\the\loopcount}
-                   \xdef\first@{\first@@}
-                \fi
-             \fi
+                \res@count=\csname res@count\the\loopcount\endcsname
+                \advance\res@count by 1
+                \ifnum\res@count=0\relax
+                   \ifx\allow@zero\n@ \advance\res@count by 1 \fi
              \fi
              \fi
+             \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+             \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
              \ifnum\loopcount=\rule@num\relax
+              \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens
+                 \innerloopcount=\rule@tens \add@to@rule@tens
+              \fi
               \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens
                 \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
                    \xdef\temp@{\rule@tens}
                 \else
                    \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
                 \fi
-                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
-                \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
-                \ifnum\innerloopcount=0
-                   \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
-                \fi
-                \xdef\rule@tens{\the\innerloopcount}
+                \xdef\ruler@{\ruler@ !<\temp@>}
               \else
-                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+                \xdef\ruler@{\ruler@ -}
               \fi
               \xdef\temp@{\csname res@count\rule@num\endcsname}
               \expandafter\ifx\csname alt@ruler\temp@\endcsname\relax
@@ -8079,7 +8637,6 @@
                 \expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@}
               \fi
              \fi
-             \ifx\hide@now\n@
              \ifx\collect@valtop\yes
              \ifnum\v@lseqtop=\loopcount
                 \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
@@ -8112,14 +8669,11 @@
              \ifnum\v@lseqbbbbottom=\loopcount
                 \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname}
              \fi\fi
-             \fi
              \ifx\collect@restop\yes
              \ifnum\tr@nsseqtop=\loopcount
                 \xdef\last@restop{\last@@restop}
                 \xdef\last@@restop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatetop{\tr@nslatetop\first@}
-                \fi
+                \xdef\tr@nslatetop{\tr@nslatetop\first@}
                 \innerloopcount=\triple@counttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8129,9 +8683,7 @@
              \ifnum\tr@nsseqttop=\loopcount
                 \xdef\last@resttop{\last@@resttop}
                 \xdef\last@@resttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatettop{\tr@nslatettop\first@}
-                \fi
+                \xdef\tr@nslatettop{\tr@nslatettop\first@}
                 \innerloopcount=\triple@countttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8140,10 +8692,8 @@
              \ifx\collect@restttop\yes
              \ifnum\tr@nsseqtttop=\loopcount
                 \xdef\last@restttop{\last@@restttop}
-                \xdef\last@@restttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
-                \fi
+                \last@@restttop{\first@}
+                \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
                 \innerloopcount=\triple@counttttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8153,9 +8703,7 @@
              \ifnum\tr@nsseqttttop=\loopcount
                 \xdef\last@resttttop{\last@@resttttop}
                 \xdef\last@@resttttop{\first@}
-                \ifx\hide@now\n@
-                   \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
-                \fi
+                \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
                 \innerloopcount=\triple@countttttop
                 \advance\innerloopcount by 1
                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8165,9 +8713,7 @@
              \ifnum\tr@nsseqbottom=\loopcount
                  \xdef\last@resbottom{\last@@resbottom}
                  \xdef\last@@resbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
-                 \fi
+                 \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
                  \innerloopcount=\triple@countbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8177,9 +8723,7 @@
              \ifnum\tr@nsseqbbottom=\loopcount
                  \xdef\last@resbbottom{\last@@resbbottom}
                  \xdef\last@@resbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
                  \innerloopcount=\triple@countbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8189,9 +8733,7 @@
              \ifnum\tr@nsseqbbbottom=\loopcount
                  \xdef\last@resbbbottom{\last@@resbbbottom}
                  \xdef\last@@resbbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
                  \innerloopcount=\triple@countbbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8201,9 +8743,7 @@
              \ifnum\tr@nsseqbbbbottom=\loopcount
                  \xdef\last@resbbbbottom{\last@@resbbbbottom}
                  \xdef\last@@resbbbbottom{\first@}
-                 \ifx\hide@now\n@
-                    \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
-                 \fi
+                 \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
                  \innerloopcount=\triple@countbbbbottom
                  \advance\innerloopcount by 1
                  \ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8218,8 +8758,7 @@
           \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{%
                            \the\innerloopcount}
          \else
-          \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi
-          \ifx\hide@now\n@
+          \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
           \ifx\collect@valtop\yes
           \ifnum\v@lseqtop=\loopcount
              \xdef\v@ltop{\v@ltop,N}
@@ -8284,31 +8823,8 @@
           \ifnum\tr@nsseqbbbbottom=\loopcount
               \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -}
           \fi\fi
-          \fi
          \fi
     \ifnum\loopcount<\seq@count \repeat
-       \ifnum\rule@num=0
-           \ifnum\cons@count=\rule@tens
-              \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
-                 \xdef\temp@{\rule@tens}
-              \else
-                 \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
-              \fi
-              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
-              \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
-              \ifnum\innerloopcount=0
-                 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
-              \fi
-              \xdef\rule@tens{\the\innerloopcount}
-           \else
-              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
-           \fi
-           \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
-           \else
-             \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
-           \fi
-       \fi
-       \ifx\hide@now\n@
          \ifx\collect@cons@graphtop\yes
                 \outerloopcount=1\relax
                 \temp@count=0\relax
@@ -8382,13 +8898,8 @@
                 \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
              \fi
          \fi
-       \fi
 
-%%%%%%%%%%%%%
-    \ifx\hide@now\y@
-       \regionalshadenowtrue \regionaltintnowtrue
-       \regionalemphnowtrue  \framenowtrue
-    \fi
+    \xdef\g@p{n}
     \ifregionalshadenow \calc@regshade \fi
     \ifregionaltintnow  \calc@regtint  \fi
     \ifregionalemphnow  \calc@regemph  \fi
@@ -8401,17 +8912,6 @@
     \ifbbottomfeaturenow   \xdef\bottop@{bbottom}   \calc@feature \fi
     \ifbbbottomfeaturenow  \xdef\bottop@{bbbottom}  \calc@feature \fi
     \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi
-    \ifx\hide@now\y@
-      \xdef\hidebar@on{1}
-      \ifnum\pos@count=\bar@pos
-      \else
-       \loopcount=\pos@count
-       \advance\loopcount by -\bar@pos
-       \xdef\bar@pos{\the\pos@count}
-       \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;}
-      \fi
-    \else
-%%%%%%%%%%%%%
     \advance\pos@count by 1
      \ifshow@logo         \calc@logo     \fi
      \ifall@fshade \all@funcshade
@@ -8427,10 +8927,31 @@
        \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi
       \fi
      \fi
-%%%%%%%%
-    \fi
-    \xdef\hide@now{n}
-%%%%%%%%
+     \ifnum\rule@num=0
+         \ifx\g@p\y@
+           \xdef\ruler@{\ruler@ -}
+         \else
+           \ifnum\cons@count=\rule@tens
+              \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+                 \xdef\temp@{\rule@tens}
+              \else
+                 \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+              \fi
+              \xdef\ruler@{\ruler@ !<\temp@>}
+              \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
+              \ifnum\innerloopcount=0
+                 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+              \fi
+              \xdef\rule@tens{\the\innerloopcount}
+           \else
+              \xdef\ruler@{\ruler@ -}
+           \fi
+           \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
+           \else
+             \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
+           \fi
+         \fi
+     \fi
     \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax
       \c@nsensus
     \else
@@ -8473,6 +8994,11 @@
            \ifnum\res@count=0
               \ifx\allow@zero\n@ \advance\res@count by 1 \fi
            \fi
+           \ifx\dom@in\y@
+              \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+              \expandafter\get@dom@count\temp@
+              \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+           \fi %%%%%%%%%%%*****
            \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
            \ifnum\rule@num=\loopcount
               \temp@count=\csname res@count\the\loopcount\endcsname
@@ -8502,10 +9028,6 @@
                      \csname sequence\the\loopcount\endcsname @}
  \ifnum\loopcount<\seq@count \repeat
  \end@count=0 \count@first \end@count=0 \xdef\start@number{0}
- \ifx\hide@now\n@
-    \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
-    \framenowfalse
- \fi
  \topfeaturenowfalse     \bottomfeaturenowfalse
  \ttopfeaturenowfalse    \bbottomfeaturenowfalse
  \tttopfeaturenowfalse   \bbbottomfeaturenowfalse
@@ -8656,6 +9178,11 @@
              \ifx\allow@zero\n@ \advance\res@count by 1 \fi
           \fi
        \fi
+       \ifx\dom@in\y@
+            \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+            \expandafter\get@dom@count\temp@
+            \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@}
+       \fi         %%%%%%%%%%*****
        \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
        \ifnames@right
           \expandafter\xdef\csname seq\the\loopcount\endcsname{%
@@ -8665,15 +9192,18 @@
               <\csname newseqname\the\loopcount\endcsname>
               \csname res@count\the\loopcount\endcsname)}
        \fi
-       \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
-                   \innerloopcount
+       \ifx\dom@in\y@
        \else
-          \res@count=\csname res@count\the\loopcount\endcsname
-          \advance\res@count by -1
-          \ifnum\res@count=0
-             \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+          \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
+                      \innerloopcount
+          \else
+             \res@count=\csname res@count\the\loopcount\endcsname
+             \advance\res@count by -1
+             \ifnum\res@count=0
+                \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+             \fi
+         \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
           \fi
-      \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
        \fi
     \else
        \ifnames@right
@@ -8683,8 +9213,16 @@
               <\csname newseqname\the\loopcount\endcsname>}
        \fi
     \fi
-    \innerloopcount=\csname res@count\the\loopcount\endcsname
-    \advance\innerloopcount by \res@perline \advance\innerloopcount by 1
+    \ifx\dom@in\y@
+         \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname}
+         \expandafter\get@dom@count\temp@
+         \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@}
+         \innerloopcount=\res@count
+    \else
+         \innerloopcount=\csname res@count\the\loopcount\endcsname
+         \advance\innerloopcount by \res@perline
+    \fi              %%%%%%%%%%%%%*****
+    \advance\innerloopcount by 1
     \ifregionalshade
          \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
          \else
@@ -9088,6 +9626,7 @@
          \def\res@@style{\csname func@style#1\endcsname}%
          \if\last@ *\def\last@{0}\fi
          \if\last@ /\def\last@{10}\fi
+         \if\last@ !\def\last@{11}\fi
    \else%
    \iffuncmode%
          \xdef\boxc@l@r{\csname fg@color#1\endcsname}%
@@ -9095,8 +9634,9 @@
          \def\res@@style{\csname func@style#1\endcsname}%
          \if\last@ *\def\last@{0}\fi
          \if\last@ /\def\last@{10}\fi
+         \if\last@ !\def\last@{11}\fi
    \else%
-   \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+   \ifcase\last@\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
              \def\res@@style{\all@style}%
          \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
              \def\res@@style{\id@style}%
@@ -9112,7 +9652,9 @@
              \def\res@@style{\csname relax\endcsname}%
          \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
              \def\res@@style{\csname relax\endcsname}%
-         \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+             \def\res@@style{\csname relax\endcsname}%
+         \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
              \def\res@@style{\csname relax\endcsname}%
    \fi\fi\fi\fi%
    \ifx\second@\comm@%
@@ -9154,6 +9696,9 @@
       \if\last@ *%
          \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
       \else%
+      \if\last@ !%
+         \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
+      \else%
       \if\last@ /%
          \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
       \else%
@@ -9178,18 +9723,22 @@
          \else
             \xdef\textc@l@r{\c@nsc@l}%
          \fi%
-      \fi\fi\fi%
+      \fi\fi\fi\fi%
       \def\res@@style{\csname relax\endcsname}%
    \else%
    \ifT@coffee%
       \if\last@ *%
          \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
       \else%
-         \if\last@ /%
-            \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \if\last@ !%
+            \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
          \else%
-            \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
-             \def\res@@style{\csname relax\endcsname}%
+            \if\last@ /%
+               \xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+            \else%
+               \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
+               \def\res@@style{\csname relax\endcsname}%
+            \fi
          \fi%
       \fi%
    \else%
@@ -9209,7 +9758,9 @@
              \def\res@@style{\csname relax\endcsname}%
          \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
              \def\res@@style{\csname relax\endcsname}%
-         \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+         \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+             \def\res@@style{\csname relax\endcsname}%
+         \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
              \def\res@@style{\csname relax\endcsname}%
    \fi\fi\fi\fi%
    \xdef\first@{#3@}%
@@ -10223,124 +10774,6 @@
    \fi%
    \fi%
 }
-\def\next@hidebar#1;#2;#3;#4@{%
-   \xdef\first@{#1}%
-   \ifx\first@\ampers@nd%
-   \else%
-      \fontfamily{\hideblock@family}\fontseries{\hideblock@series}%
-      \fontshape{\hideblock@shape}%
-      \selectfont%
-      \newline\hbox{}%
-      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
-      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
-      \hbox to -\box@width{\hss}%
-      \kern-0.1\box@width%
-      \xdef\last@{#3[,]&}\expandafter\opt@color\last@%
-      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
-      \textcolor{\f@color}{%
-      \hbox to \first@\box@width{}%
-      \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}%
-      \xdef\last@{#2[,]&}\expandafter\opt@color\last@%
-      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
-      \vspace{-0.23\box@height}%
-      \xdef\temp@{triangle}%
-      \ifx\fourth@\temp@%
-      \else
-      \xdef\temp@{square}%
-      \ifx\fourth@\temp@%
-      \else
-      \xdef\temp@{none}%
-      \ifx\fourth@\temp@%
-      \else
-      \vspace{-0.06\box@height}%
-      \fi\fi\fi%
-      \newline\hbox{}%
-      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
-      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
-      \hbox to -\box@width{\hss}%
-      \hbox to \first@\box@width{}%
-      \kern-0.1\box@width%
-      \textcolor{\f@color}{%
-      \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}%
-      \xdef\first@{triangle}%
-      \ifx\fourth@\first@%
-         \kern-0.582\box@width%
-         \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}%
-         \kern-0.418\box@width%
-      \else
-         \xdef\first@{square}%
-         \ifx\fourth@\first@%
-            \kern-0.6\box@width%
-            \raisebox{-0.12\box@height}{%
-            \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}%
-            \raisebox{-0.19\box@height}{%
-            \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
-            \kern-1.4\box@width%
-         \else
-            \xdef\first@{none}%
-            \ifx\fourth@\first@%
-               \kern-0.6\box@width%
-               \raisebox{-0.19\box@height}{%
-               \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
-               \kern-0.4\box@width%
-            \else
-               \kern-0.6\box@width%
-               \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}%
-               \kern-0.4\box@width%
-            \fi%
-         \fi%
-      \fi%
-      \kern-0.58\box@width%
-      \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}%
-      \xdef\first@{#4@}}%
-   \fi
-}
-\def\put@@hidebar{%
-   \if\first@ @%
-   \else
-      \hbox to -\box@width{\hss}%
-      \expandafter\next@hidebar\first@%
-      \put@@hidebar%
-   \fi%
-}
-\def\put@hidebar{%
-   \ifx\hide@seqs\n@%
-   \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi%
-   \temp@count=\seq@count%
-   \advance\temp@count by 1%
-   \ifx\hide@seqs\y@
-      \advance\temp@count by -1 %
-   \else%
-   \loopcount=1%
-   \xdef\first@{true}%
-   \loop%
-      \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@%
-         \advance\temp@count by -1\fi%
-      \advance\loopcount by 1%
-   \ifnum\loopcount>\seq@count\else\repeat%
-   \fi
-   \ifnum\temp@count>0%
-   \setlength\temp@@length{\box@height}%
-   \advance\temp@@length by \box@depth%
-   \setlength\arrow@height{0.5\temp@@length}%
-   \setlength\temp@@length{\temp@count\temp@@length}%
-   \advance\temp@@length by \arrow@height%
-   \advance\temp@@length by -0.75\box@height%%%%%%%
-   \setlength\arrow@width{\sep@space}%
-   \setlength\arrow@width{\seq@gap@num\arrow@width}%
-   \advance\temp@@length by \arrow@width%
-   \vspace{\arrow@height}%
-   \vspace{-\temp@@length}%
-   \vspace{-2.56\baselineskip}%
-   \xdef\first@{\stylehidebar @}%
-   \put@@hidebar%
-   \vspace{-\arrow@height}%
-   \vspace{-0.47\box@height}%
-   \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi%
-   \newline\hbox{}%
-   \fi%
-   \fi%
-}
 \def\decimal@A#1#2@{%
    \def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}%
    \xdef\temp@@{#1}%
@@ -10474,12 +10907,13 @@
       \xdef\fourth@{\fl@g\temp@}%
       \if\first@ W%
          \hbox to \box@width{\hss%
-         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{0.8}[\third@]%
+         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]%
          {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}%
          \kern-\box@width%
       \else%
-         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{1}[\third@]%
-         {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}%
+         \hbox to \box@width{\hss%
+         \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]%
+         {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}%
          \kern-\box@width%
       \fi%
       \advance\temp@count by \second@%
@@ -10778,7 +11212,7 @@
 
 \def\set@lines{%
    \pos@count=1
-   \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}%
+   \xdef\frame@pos{1}\xdef\bar@pos{0}%
    \xdef\featurepostop{1}    \xdef\featureposbottom{1}%
    \xdef\featureposttop{1}   \xdef\featureposbbottom{1}%
    \xdef\featurepostttop{1}  \xdef\featureposbbbottom{1}%
@@ -10900,9 +11334,6 @@
       \ifnum\frame@on=0 \xdef\frame@{0}\fi%
       \put@frame%
    \fi%
-   \ifnum\hidebar@on=1 %
-      \put@hidebar%
-   \fi%
    \ifshow@logo\ifnum\logo@top=1 %
       \xdef\last@{\stack@sequencelogo @}%
       \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi
@@ -11008,7 +11439,7 @@
       \fi
    \fi
    \xdef\consensus{} \xdef\ruler@{}
-   \xdef\styleframe{}         \xdef\stylehidebar{}
+   \xdef\styleframe{}
    \xdef\textfeaturetop{}     \xdef\textfeaturebottom{}
    \xdef\textfeaturettop{}    \xdef\textfeaturebbottom{}
    \xdef\textfeaturetttop{}   \xdef\textfeaturebbbottom{}
@@ -11132,7 +11563,7 @@
     \xdef\textfeaturebbottom{}   \xdef\featureonbbottom{0}
     \xdef\textfeaturebbbottom{}  \xdef\featureonbbbottom{0}
     \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0}
-    \xdef\styleframe{}        \xdef\stylehidebar{}
+    \xdef\styleframe{}
     \xdef\stylefeaturetop{}
     \xdef\stylefeaturettop{}
     \xdef\stylefeaturetttop{}
@@ -11143,6 +11574,134 @@
     \xdef\stylefeaturebbbbottom{}}
 \def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
 \def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
+\def\domain@count{%
+    \loopcount=0
+    \ifT@coffee
+       \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+       \expandafter\res@get\seq@line
+       \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+       \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+    \fi
+    \loop
+       \advance\loopcount by 1
+       \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+       \expandafter\res@get\seq@line
+       \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
+       \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+       \ifT@coffee
+          \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+          \expandafter\res@get\seq@line
+          \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+       \fi
+    \ifnum\loopcount<\seq@count\repeat
+    \ifx\first@\ampers@nd
+    \else
+     \ifnum\next@domain@num>-99999\relax
+         \ifnum\domain@seq=0
+             \temp@count=\csname dom@count0\endcsname
+             \advance\temp@count by 1
+             \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count}
+         \fi
+         \loopcount=0
+         \loop
+           \advance\loopcount by 1
+            \xdef\first@{\csname res\the\loopcount\endcsname}
+            \expandafter\check@char\first@
+            \ifletter
+               \temp@count=\csname dom@count\the\loopcount\endcsname
+               \advance\temp@count by 1
+               \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count}
+               \if\seq@type A \relax
+                  \temp@count=\char@num
+                  \ifnum\temp@count>96 \advance\temp@count by -32 \fi
+                  \ifnum\temp@count=69 \guess@protein
+                  \else
+                  \ifnum\temp@count=70 \guess@protein
+                  \else
+                  \ifnum\temp@count=73 \guess@protein
+                  \else
+                  \ifnum\temp@count=76 \guess@protein
+                  \else
+                  \ifnum\temp@count=80 \guess@protein
+                  \else
+                  \ifnum\temp@count=81 \guess@protein
+                  \fi\fi\fi\fi\fi\fi
+               \fi
+            \fi
+         \ifnum\loopcount<\seq@count\repeat
+         \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num
+            \advance\total@count by 1
+            \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
+            \loopcount=0
+            \ifx\g@p\y@
+               \ifT@coffee
+                  \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                   \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+               \fi
+            \fi
+            \ifT@coffee
+               \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+            \fi
+            \loop
+               \advance\loopcount by 1
+               \ifx\g@p\y@
+                  \ifT@coffee
+                     \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                      \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+                  \fi
+                  \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+                                   \csname sequence\the\loopcount\endcsname\equ@l}
+                  \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+                                   \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                  \ifnum\outerloopcount=0
+                     \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                      \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                  \fi
+               \fi
+               \ifT@coffee
+                  \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+                                   \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+               \fi
+               \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+                                \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
+               \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+                                \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+               \ifnum\outerloopcount=0
+                  \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                   \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+               \fi
+            \ifnum\loopcount<\seq@count\repeat
+            \expandafter\get@item\domain@num@list
+            \xdef\domain@num@list{\first@}
+            \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999}
+            \else
+               \loopcount=\next@domain@num
+               \advance\loopcount by 1
+               \ifnum\loopcount=\fourth@
+                  \xdef\g@p{n}
+               \else
+                  \xdef\g@p{y}
+                     \advance\total@count by 1
+                     \advance\outerloopcount by 1
+                     \ifnum\outerloopcount=\res@perline
+                        \outerloopcount=0
+                        \loopcount=0
+                        \loop
+                           \advance\loopcount by 1
+                           \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                                            \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+                        \ifnum\loopcount<\seq@count\repeat
+                     \fi
+               \fi
+               \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@}
+            \fi
+         \fi
+         \domain@count
+     \fi
+    \fi
+}
 \def\residue@count{%
     \expandafter\res@get\seq@line
     \if\first@\ampers@nd
@@ -11221,6 +11780,55 @@
          \fi
        \fi
     \ifeof\alignfile
+     \ifx\dom@in\y@
+       \loopcount=0
+       \ifT@coffee
+          \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+          \expandafter\get@temp\temp@
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+       \fi
+       \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+             \expandafter\get@temp\temp@
+             \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+          \fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+          \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \ifnum\loopcount<\seq@count\repeat
+       \xdef\domain@num@list{}
+       \xdef\last@{\stack@dom}
+       \get@domain
+       \xdef\domain@num@list{\domain@num@list &,@}
+       \expandafter\get@item\domain@num@list
+       \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+       \domain@count
+       \loopcount=0
+       \ifT@coffee
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+       \fi
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+          \fi
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                           \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+       \ifnum\loopcount<\seq@count\repeat
+       \if\seq@type A \guess@DNA \fi
+       \advance\seq@pointer by \total@count\relax
+       \xdef\total@pos{\the\total@count}
+
+     \else
+
        \ifnum\start@seq=0
           \xdef\seq@line{\csname sequence1\endcsname &@}
        \else
@@ -11238,9 +11846,10 @@
        \advance\total@count by \first@\relax
        \xdef\first@{\the\total@count}
        \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
-       \ifshow@sublogo \prep@sublogo \fi
-       \ifshow@logo  \prep@logo  \fi
-       \ifnum\seq@pointer>\res@perline \block@output \fi
+     \fi
+     \ifshow@sublogo \prep@sublogo \fi
+     \ifshow@logo  \prep@logo  \fi
+     \ifnum\seq@pointer>\res@perline \block@output \fi
     \else \read@loop
     \fi}
 \def\read@fasta{%
@@ -11270,6 +11879,55 @@
          \fi
        \fi
     \ifeof\alignfile
+     \ifx\dom@in\y@
+       \loopcount=0
+       \ifT@coffee
+          \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+          \expandafter\get@temp\temp@
+          \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+       \fi
+       \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+             \expandafter\get@temp\temp@
+             \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+          \fi
+          \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+          \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+       \ifnum\loopcount<\seq@count\repeat
+       \xdef\domain@num@list{}
+       \xdef\last@{\stack@dom}
+       \get@domain
+       \xdef\domain@num@list{\domain@num@list &,@}
+       \expandafter\get@item\domain@num@list
+       \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+       \domain@count
+       \loopcount=0
+       \ifT@coffee
+          \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+       \fi
+       \loop
+          \advance\loopcount by 1
+          \ifT@coffee
+             \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+          \fi
+          \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+          \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+                           \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+       \ifnum\loopcount<\seq@count\repeat
+       \if\seq@type A \guess@DNA \fi
+       \advance\seq@pointer by \total@count\relax
+       \xdef\total@pos{\the\total@count}
+
+     \else
+
        \ifnum\start@seq=0
           \xdef\seq@line{\csname sequence1\endcsname &@}
        \else
@@ -11287,9 +11945,10 @@
        \advance\total@count by \first@\relax
        \xdef\first@{\the\total@count}
        \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
-       \ifshow@sublogo \prep@sublogo \fi
-       \ifshow@logo  \prep@logo  \fi
-       \ifnum\seq@pointer>\res@perline \block@output \fi
+     \fi
+     \ifshow@sublogo \prep@sublogo \fi
+     \ifshow@logo  \prep@logo  \fi
+     \ifnum\seq@pointer>\res@perline \block@output \fi
     \else
        \read@fasta
     \fi}
@@ -11419,6 +12078,7 @@
     \fi
     \set@savedseqlength
     \loopcount=0 \xdef\seq@order{}
+    \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
@@ -11852,6 +12512,7 @@
 \xdef\res@numW{0}         \xdef\res@numX{0}
 \xdef\res@numY{0}         \xdef\res@numZ{0}
 \expandafter\xdef\csname res@num\d@t\endcsname{0}
+\expandafter\xdef\csname res@num\equ@l\endcsname{0}
 \xdef\res@corrA{0}        \xdef\res@corrB{0}
 \xdef\res@corrC{0}        \xdef\res@corrD{0}
 \xdef\res@corrE{0}        \xdef\res@corrF{0}
@@ -11866,6 +12527,7 @@
 \xdef\res@corrW{0}        \xdef\res@corrX{0}
 \xdef\res@corrY{0}        \xdef\res@corrZ{0}
 \expandafter\xdef\csname res@corr\d@t\endcsname{0}
+\expandafter\xdef\csname res@corr\equ@l\endcsname{0}
 \xdef\corr@max{0}         \xdef\do@freq@correction{n}
 \xdef\res@total{0}
 \xdef\stack@sequencelogo{} \xdef\bit@total{0}
@@ -11879,12 +12541,11 @@
 \expandafter\xdef\csname group@num1\endcsname{0}
 \expandafter\xdef\csname group@num2\endcsname{0}
 \xdef\exp@rt@num{0}       \xdef\exp@rt{n}
-\xdef\hide@true{n}        \xdef\hide@now{n}
-\xdef\hide@label{circ}
 \xdef\divref@{0}
 \xdef\all@thresh@ld{100}  \all@shadefalse
 \hidefeaturenames         \hidefeaturestylenames
 \xdef\T@coffee@ccons{n}   \xdef\T@coffee@bcons{n}
+\xdef\dom@in{no}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%                                                                      %%%%%
@@ -11917,6 +12578,8 @@
 \gapchar{.}                         %  . is printed in sequence gaps
 \gaprule{0.3pt}                     %  If a rule is printed in gaps use 0.3 pt
 \gapcolors{Black}{White}            %  Gap symbols appear `Black on White'
+\domaingaprule{1pt}                 %  If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White}        %  Domain separation line appears `Red on White'
 \numberingcolor{Black}              %  Numbering color is `Black'
 \shownumbering{right}               %  Show sequence numbering on the left
 \namescolor{Black}                  %  Names' color is `Black'
@@ -11978,10 +12641,6 @@
 \setseries{featurestyles}{md}       %  Use normal series for feature styles
 \setshape {featurestyles}{up}       %  Use upright shape for feature styles
 \setsize {featurestyles}{normalsize}%  Use normal size for feature styles
-\setfamily{hideblock}{rm}           %  Use roman family for hidden block labels
-\setseries{hideblock}{md}           %  Use normal series for hidden block labels
-\setshape {hideblock}{it}           %  Use italics shape for hidden block labels
-\setsize  {hideblock}{normalsize}   %  Use normal size for hidden block labels
 \setfamily{legend}{tt}              %  Use typewriter family for legend texts
 \setseries{legend}{md}              %  Use normal series for legend texts
 \setshape {legend}{up}              %  Use upright shape for legend texts