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authorNorbert Preining <norbert@preining.info>2021-04-07 03:01:59 +0000
committerNorbert Preining <norbert@preining.info>2021-04-07 03:01:59 +0000
commit70fe7f94e8281b0691a51754da3e2d40b1dd7732 (patch)
treef4be4cdf15aa796af9ae46eaf33d24279659cdb9 /macros/latex/contrib/texshade
parente4d1c68b2517d031bb9adc055fe19d1051c81042 (diff)
CTAN sync 202104070301
Diffstat (limited to 'macros/latex/contrib/texshade')
-rw-r--r--macros/latex/contrib/texshade/README35
-rw-r--r--macros/latex/contrib/texshade/texshade.dtx3519
-rw-r--r--macros/latex/contrib/texshade/texshade.ins6
-rw-r--r--macros/latex/contrib/texshade/texshade.pdfbin625524 -> 1075306 bytes
-rw-r--r--macros/latex/contrib/texshade/tsfaq.pdfbin77546 -> 0 bytes
-rw-r--r--macros/latex/contrib/texshade/tsfaq.tex432
6 files changed, 3518 insertions, 474 deletions
diff --git a/macros/latex/contrib/texshade/README b/macros/latex/contrib/texshade/README
index 71e52fa0c2..fe67201661 100644
--- a/macros/latex/contrib/texshade/README
+++ b/macros/latex/contrib/texshade/README
@@ -1,7 +1,6 @@
- TeXshade v1.25
+ TeXshade v1.26
>>
- >> A LaTeX package for setting nucleotide and peptide alignments,
- >> fingerprints, as well as sequence and subfamily logos.
+ >> A LaTeX package for setting nucleotide and peptide alignments.
>>
>> Setting alignments of nucleotides and peptides for publication
>> or presentation purposes is usually a time consuming two-step
@@ -27,7 +26,7 @@
>> ding modes. TeXshade combines highest flexibility and the
>> habitual TeX output quality--with reasonable time expenditure.
>>
- Copyright (C) 1999 - 2018 Eric Beitz
+ Copyright (C) 1999 - 2021 Eric Beitz
@@ -42,8 +41,7 @@
texshade.ins Batch file, run through LaTeX
texshade.dtx Docstrip archive, run twice through LaTeX
- tsfaq.tex Frequently asked questions about TeXshade
- texshade.txt This file
+ README This file
(a) FILES THAT WILL BE GENERATED FROM TEXSHADE.INS
@@ -58,6 +56,10 @@
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)
+ AQP_sequence_logo_1FX8.cmd
+ Example structure meme file
+ AQP_subfamily_logo_1FX8.cmd
+ Example structure meme file
Standard.cod Standard genetic code definitions
Ciliate.cod Ciliate macronuclear genetic code definitions
@@ -65,6 +67,8 @@
(b) FILE THAT WILL BE GENERATED FROM TEXSHADE.DTX
texshade.dvi Package documentation
+ or
+ texshade.pdf Package documentation
@@ -89,17 +93,13 @@
TeXshade needs lots of TeX's memory, so adjust your parameter set-
tings to make TeXshade feel comfortable. The documentation is a
- good test for this. (If you encounter problems texing the doc, you
- should tex and read section A of the FAQ-list (see d below) or
- download an on-line version [PDF-, DVI-, or PostScript format] at
- http://homepages.uni-tuebingen.de/beitz/)
-
+ good test for this.
+
The resulting file "texshade.dvi" can be viewed and printed using a
DVI-viewer which is able to display embedded PostScript. Another
possibility is to run "texshade.dvi" through DVIPS, a DVI to Post-
Script converter, and finally view and print the converted file
- which will be most likely "texshade.ps" with GhostView from the GNU
- free software foundation.
+ which will be most likely "texshade.ps" with GhostView from the GNU free software foundation.
TeXshade makes use of "color.sty" by David Carlisle. This style is
part of the Standard LaTeX Graphics Bundle. Usually, the bundle is
@@ -118,18 +118,11 @@
the files together.
- (d) THE FAQ LIST
-
- The FAQ list contains frequently asked questions about the package.
- Use it as a helpful source for solving problems with TeXshade. You
- get the list by simply running "tsfaq.tex" through LaTeX once.
-
-
3 - CONTACT
E-Mail: ebeitz@pharmazie.uni-kiel.de
- WWW: http://www.pharmazie.uni-kiel.de/chem/
+ WWW: https://www.pharmazie.uni-kiel.de/en/pharmceitica/
(On-line documentation and updates)
Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
Gutenbergstrasse 76, D-24118 Kiel (Germany)
diff --git a/macros/latex/contrib/texshade/texshade.dtx b/macros/latex/contrib/texshade/texshade.dtx
index adf4e661c3..2f2f4da380 100644
--- a/macros/latex/contrib/texshade/texshade.dtx
+++ b/macros/latex/contrib/texshade/texshade.dtx
@@ -10,7 +10,7 @@
% `README.txt' for further information!
%
%
-% Copyright (C) 1999-2018 Eric Beitz
+% Copyright (C) 1999-2021 Eric Beitz
% See the file texshade.txt
%
% \fi
@@ -393,11 +393,24 @@
% Postscript color samples are shown in the manual.
% }
%
-% \changes{1.25}{2011-12-01}{%
+% \changes{1.25}{2018-12-01}{%
% Corrections: aligments with many seqs produced wrong calculation
% of threshold shading, corrected.
% Introduction: new feature style |S-S| for disulfide bridges;
-% hooks in top feature lines can be drawn down to alignment.
+% hooks in top feature lines can be drawn down to alignment
+% by adding an underscore in the definition, e.g. |{_,-,}|.
+% }
+%
+% \changes{1.26}{2021-04-01}{%
+% Corrections: minor fixes;
+% Introduction: Chimera command file export for 'structure memes',
+% i.e. mapping of sequence logo and subfamily logo data
+% onto 3D protein structures;
+% new commands `structurememe', `chimeraballScale',
+% `chimeraaxisdistance', `memeRed', `memeBlue',
+% `memeYellow', `memeBlack', `memeWhite',
+% `memeStandardcolors', `chimerachain',
+% `memelabelcutoff', `echostructurefile'.
% }
%
%
@@ -440,7 +453,7 @@
% for further information, updates and on-line documentation
% see my homepage at
% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-% \date{\small v1.25; 2018/01/17\\[2pt]}
+% \date{\small v1.26; 2021/04/01\\[2pt]}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -504,6 +517,10 @@
% HMMTOP-format)\\
% \quad|AQP1_HMM.ext|\> topology information (extended,
% HMMTOP-format)\\
+% \quad|AQP_sequence_logo_1FX8.cmd|\\ \> Chimera structure meme file
+% \\
+% \quad|AQP_subfamily_logo_1FX8.cmd|\\ \> Chimera structure meme file
+% \\
% \quad|standard.cod|\> standard genetic code definitions\\
% \quad|ciliate.cod|\> ciliate macronuclear genetic code\\
% \end{tabbing}
@@ -518,6 +535,22 @@
%
%
% \subsection{Version History}
+%
+% \textbf{v1.26 2021/04/01}
+% \medskip
+%
+% \emph{Introductions:}
+% Chimera command file export option for 'structure memes'
+% was introduced,
+% i.e. mapping of sequence logo and subfamily logo data
+% onto 3D protein structures.
+% The new commands |\structurememe|,
+% |\memeRed|, |\memeBlue|,
+% |\memeYellow|, |\memeBlack|, |\memeWhite|,
+% |\memeStandardcolors|, |\chimeraaxisdistance|, |\chimerachain|, |\chimeraballScale|,
+% |\memelabelcutoff|, and |\echostructurefile|
+% handle the new feature.
+% \medskip
%
% \textbf{v1.25 2018/01/17}
% \medskip
@@ -526,7 +559,8 @@
% of threshold shading,\footnote{Noted by Kathryn Parker.} corrected; minor bug fixes.
%
% \emph{Introduction}: A new feature style |S-S| for disulfide bridges is
-% implemented; hooks in top feature lines can be drawn down to alignment.
+% implemented; hooks in top feature lines can be drawn down to alignment
+% by adding an underscore in the definition, e.g. |{_,-,}|.
% \medskip
%
% \textbf{v1.24 2011/12/01}
@@ -1950,6 +1984,20 @@
% \end{texshade}
% \end{verbatim}}
%
+%
+%
+% \subsection{Structure memes}
+%
+% The calculated sequence logo and subfamily logo data can
+% be used to generate \emph{Structure memes}. This a type of 3D protein
+% display that visualizes the residue composition and frequency and the
+% information content of each sequence position. Therefore, in the structure file,
+% a color code is projected onto a sphere at the $\alpha$-carbon position,
+% which is scaled according to the information content. \TeXshade\
+% generates an output file for the molecular structure display software
+% Chimera. See the files |AQP_sequence_logo_1FX8.cmd| and
+% |AQP_subfamily_logo_1FX8.cmd| generated from |texshade.dtx|.
+%
%
%
%
@@ -3025,6 +3073,54 @@
% |\showrelevance[Blue]{$\nabla$}|. The symbol will be hidden with
% |\hiderelevance|.
%
+%
+%
+% \subsubsection{Structure memes}
+%
+% \label{Lmemes}
+%
+% Structure memes combine sequence logo and subfamily logo
+% information with 3D protein structure data. \TeXshade{} generates
+% a `command file' output that can be loaded into the molecular
+% structure display software Chimera.
+%
+% A sequence logo or subfamily logo must be calculated as described in
+% the two subsections above. Then, the command
+% |\structurememe[|\meta{seqref}|]{|\meta{filename}|}| generates an
+% Chimera output file (use the ending |.cmd| or |.com|) with
+% \meta{seqref} as the reference sequence for which a protein structure
+% file must be available for display. Two example files are distributed with
+% this \TeXshade{} version to load into Chimera; the PDB file 1FX8 must
+% be used for the structure meme.
+%
+% The |\memeStandardcolors| are: |DE| (Red), |CGNQSTY| (Yellow),
+% |HKR| (Blue), |APV| (White), |FILMW| (Black).
+%
+% The color grouping can be changed using |\memeRed{|\meta{residues}|}|,
+% and accordingly |\memeYellow|, |\memeBlue|,
+% |\memeWhite|, and |\memeBlack|. If a 3D structure file contains
+% more than one chain, the structure meme display can be
+% restricted to one chain using |\chimerachain{|\meta{chainlabel}|}| with
+% \meta{chainlabel} typically being a letter e.g. |{A}|. For the radius of the
+% $\alpha$-carbon spheres the logo information bit-value is used, which can
+% be scaled using |\chimeraballScale{|\meta{factor}|}| with \meta{factor}
+% from 0--1. The residue composition at a sequence position is stored in
+% a name label of the command file and will be visible in Chimera when
+% pointing to it. To eliminate irrelevant residues a cut-off bit-value can be
+% set |\memelabelcutoff{|\meta{bit-value}|}|. The symbols |>| |:| and |.|
+% indicate the 3, 2, and 1 bit levels.
+%
+% Structure memes from subfamily logos will duplicate the structure model
+% and shift it by 40 \AA{} along the x-axis to achieve a side-by-side arrangement.
+% The translational direction can be changed using
+% |\chimeraxisdistance{|\meta{x-dist}|}{|\meta{y-dist}|}{|\meta{z-dist}|}| in
+% \AA{}ngstr\o{}m.
+%
+% Eventually, with |\echostructurefile{|\meta{strucref}|}| a reference to a
+% suitable structure file, e.g. from the PDB, can be named, which will be put
+% into the command file and which will appear when Chimera asks for a
+% structure file in a load dialog window.
+%
% \subsection{Appearance of the sequence lines}
%
% \label{seqlines}
@@ -3875,6 +3971,9 @@
% (|-=<',|$\vert$o), the middle-characters (|-=|),
% and the right-end-characters (|-=>',|$\vert$o) are
% allowed and produce the desired arrow or bar.
+% Adding an underscore in the definition for top feature hooks,
+% e.g. |{_,-,}| makes the hooks
+% fully reach down to the alignment.
% The color is changed as described above.
% \label{Lfeaturerule} The thickness can be generally
% set by the separate command |\featurerule{|\meta{length}|}|
@@ -5795,6 +5894,50 @@
% \quad|\hiderelevance|
% \hfill[\pageref{Lhiderelevance}]
%
+%
+%
+% \vspace{1.5\baselineskip}
+%
+% \textbf{Structure memes}
+% \medskip
+%
+% \quad|\structurememe[|\meta{seqref}|]{|\meta{filename}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeStandardcolors|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeRed{|\meta{residues}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeYellow{|\meta{residues}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeBlue{|\meta{residues}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeWhite{|\meta{residues}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memeBlack{|\meta{residues}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\chimerachain{|\meta{chainlabel}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\chimeraballScale{|\meta{factor}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\memelabelcutoff{|\meta{bit-value}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\chimeraxisdistance{|\meta{x-dist}|}{|\meta{y-dist}|}{|\meta{z-dist}|}|
+% \hfill[\pageref{Lmemes}]
+%
+% \quad|\echostructurefile{|\meta{strucref}|}|
+% \hfill[\pageref{Lmemes}]
+%
+%
%
% \vspace{1.5\baselineskip}
%
@@ -6159,7 +6302,7 @@
%
% \vspace{1.5\baselineskip}
%
-% \newpage
+%
%
% \textbf{Including secondary structure information}
% \medskip
@@ -6437,8 +6580,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)]
-\message{Package `texshade', Version 1.25 of 2018/01/17.}
+\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)]
+\message{Package `texshade', Version 1.26 of 2021/04/01.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -6480,6 +6623,7 @@
\newread\structurefile \newwrite\featurefile
\newread\alignfile \newread\sublogofile
\newwrite\exp@rtfile
+\newwrite\exp@rt@chimerafile
\expandafter\ifx\csname blacktriangleright\endcsname\relax
\openin\structurefile = amssymb.sty
@@ -7104,6 +7248,16 @@
\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N}
\xdef\HydroY{9} \xdef\HydroZ{N}
+\xdef\hardnessA{98} \xdef\hardnessB{0} \xdef\hardnessC{37}
+\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48}
+\xdef\hardnessG{92} \xdef\hardnessH{50} \xdef\hardnessI{98}
+\xdef\hardnessJ{86} \xdef\hardnessK{73} \xdef\hardnessL{98}
+\xdef\hardnessM{25} \xdef\hardnessN{86} \xdef\hardnessO{0}
+\xdef\hardnessP{91} \xdef\hardnessQ{95} \xdef\hardnessR{69}
+\xdef\hardnessS{94} \xdef\hardnessT{98} \xdef\hardnessU{-34}
+\xdef\hardnessV{98} \xdef\hardnessW{0} \xdef\hardnessX{0}
+\xdef\hardnessY{28} \xdef\hardnessZ{0}
+
\xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0}
@@ -9327,8 +9481,17 @@
\funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
\funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
\else
+ \xdef\second@{hardness}
+ \ifx\temp@\second@
+ \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up}
+ \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up}
+ \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up}
+ \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up}
+ \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
+ \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
+ \else
\message{<Unknown shading mode - clearing `funcgroups'>}
- \fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi
}
\def\shadeallresidues{\all@fshadetrue}
\def\get@fromstack#1;#2;#3;#4;#5@{%
@@ -12836,7 +12999,17 @@
\logocolor{EQ}{RoyalPurple}
\logocolor{R}{RedViolet}
\logocolor{K}{Black}
- \fi\fi\fi\fi\fi\fi\fi
+ \else
+ \xdef\second@{hardness}
+ \ifx\first@\second@
+ \clearlogocolors
+ \logocolor{ADEGILPQSTV}{BlueRed5}
+ \logocolor{KN}{BlueRed20}
+ \logocolor{R}{BlueRed40}
+ \logocolor{CFH}{BlueRed60}
+ \logocolor{MY}{BlueRed80}
+ \logocolor{W}{BlueRed100}
+ \fi\fi\fi\fi\fi\fi\fi\fi
}
\newcommand\findsubfamily[2][n]{%
\xdef\first@{#1}
@@ -16898,6 +17071,7 @@
\fi
\fi
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi
\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
@@ -17041,6 +17215,7 @@
\the\innerloopcount}
\else
\ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi
\ifx\collect@valtop\yes
\ifnum\v@lseqtop=\loopcount
\xdef\v@ltop{\v@ltop,N}
@@ -19324,9 +19499,628 @@
\divide\loopcount by 100 %
\xdef\third@{\the\loopcount}%
}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}}
+\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}}
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}}
+\def\memelabelcutoff#1{%
+ \xdef\label@threshold@lower{#1}
+ \setlength\temp@@length{1000sp}
+ \setlength\temp@@length{\label@threshold@lower\temp@@length}
+ \loopcount=\temp@@length
+ \xdef\label@threshold@lowerIOOO{\the\loopcount}
+ \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount}
+}
+\def\chimera@color@get#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers@nd
+ \else
+ \ifnum`#1>96 \make@upper\fi
+ \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi
+ \expandafter\chimera@color@get\third@
+ \fi
+}
+\def\memered#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{red}
+ \expandafter\chimera@color@get\third@
+}
+\def\memeblue#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{blue}
+ \expandafter\chimera@color@get\third@
+}
+\def\memeyellow#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{yellow}
+ \expandafter\chimera@color@get\third@
+}
+\def\memeblack#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{black}
+ \expandafter\chimera@color@get\third@
+}
+\def\memewhite#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{white}
+ \expandafter\chimera@color@get\third@
+}
+\def\memenone#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{none}
+ \expandafter\chimera@color@get\third@
+}
+\def\memeRed#1{\memered{#1}}
+\def\memeBlue#1{\memeblue{#1}}
+\def\memeYellow#1{\memeyellow{#1}}
+\def\memeBlack#1{\memeblack{#1}}
+\def\memeWhite#1{\memewhite{#1}}
+\def\memeNone#1{\memenone{#1}}
+\def\chimera@colors#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers@nd
+ \else
+ \xdef\second@{\csname chimera@col@\first@\endcsname}
+ \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@}
+ \expandafter\chimera@colors\third@
+ \fi
+}
+\def\memeStandardcolors{%
+ \xdef\chimera@col@A{white}
+ \xdef\chimera@col@B{none}
+ \xdef\chimera@col@C{yellow}
+ \xdef\chimera@col@D{red}
+ \xdef\chimera@col@E{red}
+ \xdef\chimera@col@F{black}
+ \xdef\chimera@col@G{yellow}
+ \xdef\chimera@col@H{blue}
+ \xdef\chimera@col@I{black}
+ \xdef\chimera@col@J{none}
+ \xdef\chimera@col@K{blue}
+ \xdef\chimera@col@L{black}
+ \xdef\chimera@col@M{black}
+ \xdef\chimera@col@N{yellow}
+ \xdef\chimera@col@O{none}
+ \xdef\chimera@col@P{white}
+ \xdef\chimera@col@Q{yellow}
+ \xdef\chimera@col@R{blue}
+ \xdef\chimera@col@S{yellow}
+ \xdef\chimera@col@T{yellow}
+ \xdef\chimera@col@U{none}
+ \xdef\chimera@col@V{white}
+ \xdef\chimera@col@W{black}
+ \xdef\chimera@col@X{none}
+ \xdef\chimera@col@Y{yellow}
+ \xdef\chimera@col@Z{none}
+}
+\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}}
+\def\chimerachain#1{\xdef\chimerach@in{.#1}}
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12
+\newcommand{\structurememe}[2][chimera.cmd]{%
+ \ifx\exp@rt@chimera\n@
+ \xdef\first@{"2 @} \expandafter\check@letter\first@
+ \xdef\first@{"2} \ifletter \get@name@number \fi
+ \xdef\chimera@seqnum{\first@}
+ \xdef\exp@rt@chimera{y}
+ \xdef\first@{"1}
+ \immediate\openout\exp@rt@chimerafile = \first@
+ \fi
+}
+\def\init@chimera@file{%
+ \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{}
+ \xdef\chimera@list@none{}
+ \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
+ \expandafter\chimera@colors\first@
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O ¡ o STRUCTURE MEME ¡ . O o}
+ \immediate\write\exp@rt@chimerafile{###}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
+ \immediate\write\exp@rt@chimerafile{###}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
+ \immediate\write\exp@rt@chimerafile{###}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{close session; background solid white;}
+ \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
+ \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface}
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0}
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca}
+ \immediate\write\exp@rt@chimerafile{}
+ \ifshow@sublogo
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{combine #0}
+ \ifnum\chimera@xdist@nce>0
+ \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera@ydist@nce>0
+ \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera@zdist@nce>0
+ \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1}
+ \fi
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{wait; focus #0#1}
+ \ifx\sublogo@name@user\ampers@nd
+ \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0}
+ \else
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0}
+ \fi
+ \xdef\first@{\sublogo@name@neg &}
+ \ifx\first@\ampers@nd
+ \immediate\write\exp@rt@chimerafile{setattr m name remaining #1}
+ \else
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1}
+ \fi
+ \else
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
+ \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
+ \ifx\logo@name@user\ampers@nd
+ \immediate\write\exp@rt@chimerafile{setattr m name logo #0}
+ \else
+ \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0}
+ \fi
+ \fi
+ \immediate\write\exp@rt@chimerafile{}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
+ \immediate\write\exp@rt@chimerafile{############################################################}
+}
+\def\make@HEX{%
+ \xdef\sixth@{\the\loopcount}%
+ \divide\loopcount by 4096\relax%
+ \ifnum\loopcount=10\relax%
+ \xdef\seventh@{A}%
+ \else%
+ \ifnum\loopcount=11\relax%
+ \xdef\seventh@{B}%
+ \else%
+ \ifnum\loopcount=12\relax%
+ \xdef\seventh@{C}%
+ \else%
+ \ifnum\loopcount=13\relax%
+ \xdef\seventh@{D}%
+ \else%
+ \ifnum\loopcount=14\relax%
+ \xdef\seventh@{E}%
+ \else%
+ \ifnum\loopcount>14\relax%
+ \xdef\seventh@{F}%
+ \else%
+ \xdef\seventh@{\the\loopcount}%
+ \fi\fi\fi\fi\fi\fi%
+ \multiply\loopcount by -4096\relax%
+ \advance\loopcount by \sixth@%
+ \xdef\sixth@{\the\loopcount}%
+ \divide\loopcount by 256\relax%
+ \ifnum\loopcount=10 \relax%
+ \xdef\eighth@{A}%
+ \else%
+ \ifnum\loopcount=11 \relax%
+ \xdef\eighth@{B}%
+ \else%
+ \ifnum\loopcount=12 \relax%
+ \xdef\eighth@{C}%
+ \else%
+ \ifnum\loopcount=13 \relax%
+ \xdef\eighth@{D}%
+ \else%
+ \ifnum\loopcount=14 \relax%
+ \xdef\eighth@{E}%
+ \else%
+ \ifnum\loopcount>14 \relax%
+ \xdef\eighth@{F}%
+ \else%
+ \xdef\eighth@{\the\loopcount}%
+ \fi\fi\fi\fi\fi\fi%
+ \xdef\seventh@{\seventh@\eighth@}%
+ \multiply\loopcount by -256\relax%
+ \advance\loopcount by \sixth@%
+ \xdef\sixth@{\the\loopcount}%
+ \divide\loopcount by 16\relax%
+ \ifnum\loopcount=10\relax%
+ \xdef\eighth@{A}%
+ \else%
+ \ifnum\loopcount=11\relax%
+ \xdef\eighth@{B}%
+ \else%
+ \ifnum\loopcount=12\relax%
+ \xdef\eighth@{C}%
+ \else%
+ \ifnum\loopcount=13\relax%
+ \xdef\eighth@{D}%
+ \else%
+ \ifnum\loopcount=14\relax%
+ \xdef\eighth@{E}%
+ \else%
+ \ifnum\loopcount>14\relax%
+ \xdef\eighth@{F}%
+ \else%
+ \xdef\eighth@{\the\loopcount}%
+ \fi\fi\fi\fi\fi\fi%
+ \xdef\seventh@{\seventh@\eighth@}%
+ \multiply\loopcount by -16\relax%
+ \advance\loopcount by \sixth@\relax%
+ \ifnum\loopcount=10\relax%
+ \xdef\eighth@{A}%
+ \else%
+ \ifnum\loopcount=11\relax%
+ \xdef\eighth@{B}%
+ \else%
+ \ifnum\loopcount=12\relax%
+ \xdef\eighth@{C}%
+ \else%
+ \ifnum\loopcount=13\relax%
+ \xdef\eighth@{D}%
+ \else%
+ \ifnum\loopcount=14\relax%
+ \xdef\eighth@{E}%
+ \else%
+ \ifnum\loopcount>14\relax%
+ \xdef\eighth@{F}%
+ \else%
+ \xdef\eighth@{\the\loopcount}%
+ \fi\fi\fi\fi\fi\fi%
+ \xdef\seventh@{\seventh@\eighth@}%
+}
+\def\write@chimera@data{%
+ \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi%
+ \loopcount=\temp@count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else%
+ \expandafter\decimal@E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=\chimera@subfamily@col@black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp@count%
+ \xdef\chimera@subfamily@col@black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera@subfamily@col@black%
+ \xdef\temp@@{\the\loopcount}%
+%%%%%%%%%%%%%%
+% * This code was taken from:
+% *
+% * Color Space - A RGB to RYB converter.
+% *
+% * Copyright (C) 2013 Joshua Gentry
+% *
+% * This program is free software: you can redistribute it and/or modify
+% * it under the terms of the GNU Affero General Public License as
+% * published by the Free Software Foundation, either version 3 of the
+% * License, or (at your option) any later version.
+%. *
+% * This program is distributed in the hope that it will be useful,
+% * but WITHOUT ANY WARRANTY; without even the implied warranty of
+% * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% * GNU Affero General Public License for more details.
+%. *
+% * You should have received a copy of the GNU Affero General Public License
+% * along with this program. If not, see <http://www.gnu.org/licenses/>.
+% */
+% RgbRyb.prototype.setRyb = function(iRed, iYellow, iBlue)
+% {
+% //-----------------------------------------------------------------------------------------
+% // Validate the arguments.
+% VALIDATOR.validate(E10002, "setRyb", arguments, [
+% {type: "number", max: 255, min: 0, arrayType: "int"},
+% {type: "number", max: 255, min: 0, arrayType: "int"},
+% {type: "number", max: 255, min: 0, arrayType: "int"}
+% ]);
+%
+% //-----------------------------------------------------------------------------------------
+% // Save the RYB
+% this.pRyb = [iRed, iYellow, iBlue];
+%
+% // Remove the whiteness from the color.
+% var iWhite = Math.min(iRed, iYellow, iBlue);
+%
+% iRed -= iWhite;
+% iYellow -= iWhite;
+% iBlue -= iWhite;
+%
+% var iMaxYellow = Math.max(iRed, iYellow, iBlue);
+%
+% // Get the green out of the yellow and blue
+% var iGreen = Math.min(iYellow, iBlue);
+%
+% iYellow -= iGreen;
+% iBlue -= iGreen;
+%
+% if (iBlue > 0 && iGreen > 0)
+% {
+% iBlue *= 2.0;
+% iGreen *= 2.0;
+% }
+%
+% // Redistribute the remaining yellow.
+% iRed += iYellow;
+% iGreen += iYellow;
+%
+% // Normalize to values.
+% var iMaxGreen = Math.max(iRed, iGreen, iBlue);
+%
+% if (iMaxGreen > 0)
+% {
+% var iN = iMaxYellow / iMaxGreen;
+%
+% iRed *= iN;
+% iGreen *= iN;
+% iBlue *= iN;
+% }
+%
+% // Add the white back in.
+% iRed += iWhite;
+% iGreen += iWhite;
+% iBlue += iWhite;
+%
+% // Save the RGB
+% this.pRgb = [Math.floor(iRed), Math.floor(iGreen), Math.floor(iBlue)];
+% }
+%%%%%%%%%%%%%%
+ \loopcount=\chimera@subfamily@col@blue\relax%
+ \ifnum\chimera@subfamily@col@yellow>\loopcount\relax%
+ \loopcount=\chimera@subfamily@col@yellow\relax%
+ \else%
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax%
+ \loopcount=\chimera@subfamily@col@red\relax%
+ \fi%
+ \fi%
+ \xdef\max@yellow{\the\loopcount}%
+ \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax%
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}%
+ \else%
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}%
+ \fi%
+ \loopcount=\chimera@subfamily@col@yellow\relax%
+ \advance\loopcount by -\chimera@subfamily@col@green%
+ \xdef\chimera@subfamily@col@yellow{\the\loopcount}%
+ \loopcount=\chimera@subfamily@col@blue\relax%
+ \advance\loopcount by -\chimera@subfamily@col@green%
+ \xdef\chimera@subfamily@col@blue{\the\loopcount}%
+ \ifnum\chimera@subfamily@col@blue>0\relax%
+ \ifnum\chimera@subfamily@col@green>0\relax%
+ \loopcount=\chimera@subfamily@col@blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}%
+ \loopcount=\chimera@subfamily@col@green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera@subfamily@col@green\relax%
+ \advance\loopcount by \chimera@subfamily@col@yellow%
+ \xdef\chimera@subfamily@col@green{\the\loopcount}%
+ \loopcount=\chimera@subfamily@col@red\relax%
+ \advance\loopcount by \chimera@subfamily@col@yellow%
+ \xdef\chimera@subfamily@col@red{\the\loopcount}%
+ \loopcount=\chimera@subfamily@col@blue\relax%
+ \ifnum\chimera@subfamily@col@green>\loopcount\relax%
+ \loopcount=\chimera@subfamily@col@green\relax%
+ \else%
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax%
+ \loopcount=\chimera@subfamily@col@red\relax%
+ \fi%
+ \fi%
+ \xdef\max@green{\the\loopcount}%
+ \loopcount=\chimera@subfamily@col@blue%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@subfamily@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera@subfamily@col@green%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@subfamily@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera@subfamily@col@red%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@subfamily@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera@labelOne@set\n@%
+ \xdef\chimera@labelOne@set{y}%
+ \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
+ \fi%
+ \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
+ \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
+ \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}%
+ \ifshow@sublogo
+ \ifnum\temp@@count>0 \else\temp@@count=1\fi%
+ \loopcount=\temp@@count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else%
+ \expandafter\decimal@E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=-\chimera@remaining@col@red\relax%
+ \xdef\chimera@remaining@col@red{\the\loopcount}%
+ \loopcount=-\chimera@remaining@col@yellow\relax%
+ \xdef\chimera@remaining@col@yellow{\the\loopcount}%
+ \loopcount=-\chimera@remaining@col@blue\relax%
+ \xdef\chimera@remaining@col@blue{\the\loopcount}%
+ \loopcount=-\chimera@remaining@col@white\relax%
+ \xdef\chimera@remaining@col@white{\the\loopcount}%
+ \loopcount=-\chimera@remaining@col@black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp@count%
+ \xdef\chimera@remaining@col@black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera@remaining@col@black%
+ \xdef\temp@@{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@blue\relax%
+ \ifnum\chimera@remaining@col@yellow>\loopcount\relax%
+ \loopcount=\chimera@remaining@col@yellow\relax%
+ \else%
+ \ifnum\chimera@remaining@col@red>\loopcount\relax%
+ \loopcount=\chimera@remaining@col@red\relax%
+ \fi%
+ \fi%
+ \xdef\max@yellow{\the\loopcount}%
+ \ifnum\chimera@remaining@col@blue<\chimera@remaining@col@yellow\relax%
+ \xdef\chimera@remaining@col@green{\chimera@remaining@col@blue}%
+ \else%
+ \xdef\chimera@remaining@col@green{\chimera@remaining@col@yellow}%
+ \fi%
+ \loopcount=\chimera@remaining@col@yellow\relax%
+ \advance\loopcount by -\chimera@remaining@col@green%
+ \xdef\chimera@remaining@col@yellow{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@blue\relax%
+ \advance\loopcount by -\chimera@remaining@col@green%
+ \xdef\chimera@remaining@col@blue{\the\loopcount}%
+ \ifnum\chimera@remaining@col@blue>0\relax%
+ \ifnum\chimera@remaining@col@green>0\relax%
+ \loopcount=\chimera@remaining@col@blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@blue{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera@remaining@col@green\relax%
+ \advance\loopcount by \chimera@remaining@col@yellow%
+ \xdef\chimera@remaining@col@green{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@red\relax%
+ \advance\loopcount by \chimera@remaining@col@yellow%
+ \xdef\chimera@remaining@col@red{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@blue\relax%
+ \ifnum\chimera@remaining@col@green>\loopcount\relax%
+ \loopcount=\chimera@remaining@col@green\relax%
+ \else%
+ \ifnum\chimera@remaining@col@red>\loopcount\relax%
+ \loopcount=\chimera@remaining@col@red\relax%
+ \fi%
+ \fi%
+ \xdef\max@green{\the\loopcount}%
+ \loopcount=\chimera@remaining@col@blue%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@remaining@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera@remaining@col@green%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@remaining@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera@remaining@col@red%
+ \ifnum\max@green>0\relax%
+ \multiply\loopcount by \max@yellow%
+ \divide\loopcount by \max@green%
+ \fi%
+ \advance\loopcount by \chimera@remaining@col@white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp@count%
+ \make@HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera@label@remainingOne@set\n@%
+ \xdef\chimera@label@remainingOne@set{y}%
+ \xdef\chimera@label@remaining{.\chimera@label@remaining}%
+ \fi%
+ \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
+ \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
+ \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@remaining' #1:\chimera@res@num\chimerach@in @ca}%
+ \fi%
+}
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13
+\def\get@chimera@res@num#1,#2@{\xdef\chimera@res@num{#1}\xdef\chimera@stack{#2}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines end %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\next@logo#1:#2,#3@{%
\xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
\ifx\first@\ampers@nd%
+ \ifx\exp@rt@chimera\y@%
+ \xdef\chimera@stack{\chimera@stack @}%
+ \expandafter\get@chimera@res@num\chimera@stack%
+ \ifx\chimera@res@num\ampers@nd%
+ \else%
+ \write@chimera@data%
+ \fi%
+ \xdef\chimera@label@subfamily{}%
+ \xdef\chimera@label@remaining{}%
+ \xdef\chimera@subfamily@col@red{0}%
+ \xdef\chimera@subfamily@col@blue{0}%
+ \xdef\chimera@subfamily@col@yellow{0}%
+ \xdef\chimera@subfamily@col@black{0}%
+ \xdef\chimera@subfamily@col@white{0}%
+ \xdef\chimera@remaining@col@red{0}%
+ \xdef\chimera@remaining@col@blue{0}%
+ \xdef\chimera@remaining@col@yellow{0}%
+ \xdef\chimera@remaining@col@black{0}%
+ \xdef\chimera@remaining@col@white{0}%
+ \xdef\chimera@labelOne@set{n}%
+ \xdef\chimera@labelTwo@set{n}%
+ \xdef\chimera@labelThree@set{n}%
+ \xdef\chimera@label@remainingOne@set{n}%
+ \xdef\chimera@label@remainingTwo@set{n}%
+ \xdef\chimera@label@remainingThree@set{n}%
+ \fi%
\ifx\clear@logo\n@%
\ifx\hide@sig\n@%
\expandafter\firstchar@get\sublogo@sig%
@@ -19348,12 +20142,10 @@
\fi%
\fi%
\temp@count=0%
+ \temp@@count=0%
\kern\box@width%
\advance\outerloopcount by 1 %
\else%
- \ifnum#2=1%
- \temp@count=0%
- \else%
\if\seq@type N%
\loopcount=\second@%
\multiply\loopcount by 2%
@@ -19389,7 +20181,7 @@
\fi\fi\fi\fi%
\xdef\third@{\fl@g\temp@}%
\ifnum\temp@count<0 %
- \ifnum\second@<0 \else\temp@count=0 \fi%
+ \ifnum\second@<0 \else\temp@@count=-\temp@count\relax\temp@count=0 \fi%
\fi%
\ifnum\temp@count>0 %
\loopcount=\temp@count \xdef\fl@g{}%
@@ -19416,7 +20208,64 @@
\kern-\box@width%
\fi%
\advance\temp@count by \second@%
- \fi%
+ \xdef\temp@{\the\temp@count}%
+ \ifx\exp@rt@chimera\y@%
+ \xdef\temp@@{\csname chimera@col@\first@\endcsname}%
+ \ifnum\second@<0 %
+ \xdef\temp@@@{\csname chimera@remaining@col@\temp@@\endcsname}%
+ \temp@count=\temp@@@%
+ \advance\temp@count by \second@%
+ \expandafter\xdef\csname chimera@remaining@col@\temp@@\endcsname{\the\temp@count}%
+ \ifnum\second@<\label@threshold@lowerremainingIOOO%
+ \ifnum\second@<-999%
+ \ifx\chimera@label@remainingOne@set\n@%
+ \xdef\chimera@label@remainingOne@set{y}%
+ \xdef\chimera@label@remaining{.\chimera@label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-1999%
+ \ifx\chimera@label@remainingTwo@set\n@%
+ \xdef\chimera@label@remainingTwo@set{y}%
+ \xdef\chimera@label@remaining{:\chimera@label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-2999%
+ \ifx\chimera@label@remainingThree@set\n@%
+ \xdef\chimera@label@remainingThree@set{y}%
+ \xdef\chimera@label@remaining{>\chimera@label@remaining}%
+ \fi%
+ \fi%
+ \xdef\chimera@label@remaining{\first@\chimera@label@remaining}%
+ \fi%
+ \else%
+ \xdef\temp@@@{\csname chimera@subfamily@col@\temp@@\endcsname}%
+ \temp@count=\temp@@@%
+ \advance\temp@count by \second@%
+ \expandafter\xdef\csname chimera@subfamily@col@\temp@@\endcsname{\the\temp@count}%
+ \ifnum\second@>\label@threshold@lowerIOOO%
+ \ifnum\second@>999%
+ \ifx\chimera@labelOne@set\n@%
+ \xdef\chimera@labelOne@set{y}%
+ \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>1999%
+ \ifx\chimera@labelTwo@set\n@%
+ \xdef\chimera@labelTwo@set{y}%
+ \xdef\chimera@label@subfamily{:\chimera@label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>2999%
+ \ifx\chimera@labelThree@set\n@%
+ \xdef\chimera@labelThree@set{y}%
+ \xdef\chimera@label@subfamily{>\chimera@label@subfamily}%
+ \fi%
+ \fi%
+ \xdef\chimera@label@subfamily{\first@\chimera@label@subfamily}%
+ \fi%
+ \fi%
+ \fi%
+ \temp@count=\temp@%
\fi%
\xdef\temp@{\last@.}%
\ifx\temp@\d@t%
@@ -19926,8 +20775,7 @@
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
-% \vspace{-\bar@length}%%%%%%%%%%%%%%%%%%%%%%%
- \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%%
+ \setlength{\bar@length}{0pt}%
\put@feature%
\temp@@count=\b@feature@count%
\advance\temp@@count by 1%
@@ -20680,6 +21528,7 @@
\fi
\ifshow@sublogo \closein\sublogofile \fi
\ifx\exp@rt\y@ \closeout\exp@rtfile \fi
+ \ifx\exp@rt@chimera\y@ \closeout\exp@rt@chimerafile \fi%
\closein\alignfile
\message{)}
}
@@ -20832,8 +21681,6 @@
\ifnum\loopcount<\seq@count \repeat
\xdef\seq@order{\seq@order,@}
\killseq@count=\seq@count
-% \seq@percent=100
-% \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
\fi
\fi
}
@@ -21105,6 +21952,14 @@
\xdef\thresh@ld@{\the\loopcount}
\loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
\xdef\all@thresh@ld@{\the\loopcount}
+ \if\exp@rt@chimera\y@%
+ \ifshow@logo%
+ \init@chimera@file%
+ \else%
+ \ifshow@sublogo%
+ \init@chimera@file%
+ \fi\fi%
+ \fi%
\bgroup
\ifx\out@put\y@\bigskip\fi
\iffuncmode \show@consfalse \fi
@@ -21262,6 +22117,32 @@
\expandafter\xdef\csname group@num1\endcsname{0}
\expandafter\xdef\csname group@num2\endcsname{0}
\xdef\exp@rt@num{0} \xdef\exp@rt{n}
+\xdef\exp@rt@chimera@num{1} \xdef\exp@rt@chimera{n} \xdef\chimera@stack{}
+\xdef\chimerab@llSc@le{1.0}
+\memelabelcutoff{0.1}
+\xdef\chimera@labelOne@set{n}
+\xdef\chimera@labelTwo@set{n}
+\xdef\chimera@labelThree@set{n}
+\xdef\chimera@labelOne@remaining@set{n}
+\xdef\chimera@labelTwo@remaining@set{n}
+\xdef\chimera@labelThree@remaining@set{n}
+\xdef\chimera@xdist@nce{0} \xdef\chimera@ydist@nce{40} \xdef\chimera@zdist@nce{0}
+\xdef\chimerach@in{} \xdef\chimera@seqnum{0}
+\xdef\chimera@label@subfamily{} \xdef\chimera@label@remaining{}
+\memeStandardcolors
+\xdef\chimera@subfamily@col@red{0}%
+\xdef\chimera@subfamily@col@blue{0}%
+\xdef\chimera@subfamily@col@yellow{0}%
+\xdef\chimera@subfamily@col@black{0}%
+\xdef\chimera@subfamily@col@white{0}%
+\xdef\chimera@subfamily@col@none{0}%
+\xdef\chimera@remaining@col@red{0}%
+\xdef\chimera@remaining@col@blue{0}%
+\xdef\chimera@remaining@col@yellow{0}%
+\xdef\chimera@remaining@col@black{0}%
+\xdef\chimera@remaining@col@white{0}%
+\xdef\chimera@remaining@col@none{0}%
+\xdef\echo@filename{}
\xdef\divref@{0}
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
@@ -24118,6 +24999,2606 @@ cons 301 23322--32222222223--3222223233322122-111112221------223 355
%</TCoffee>
% \end{macrocode}
% \begin{macrocode}
+%<*AQPlogo>
+############################################################
+###
+### . O ¡ o STRUCTURE MEME ¡ . O o
+###
+### Chimera command file generated from TeXshade logo data
+### use '.cmd' or '.com' suffix
+###
+### Reference sequence: 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8
+###
+############################################################
+
+############################################################
+### residue colors: (set with \memeRed{residues} etc.)
+### DE (Red)
+### HKR (Blue)
+### CGNQSTY (Yellow)
+### FILMW (Black)
+### APV (White)
+############################################################
+
+############################################################
+### residues in labels: (\memelabelcutoff{bit-value})
+### 0.1 bit required to appear
+### > : . indicate 3, 2, and 1 bit levels
+############################################################
+
+############################################################
+### initialize & load structure
+############################################################
+close session; background solid white;
+echo load structure file for 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8
+open #0; ~ribbon; ~surface
+
+############################################################
+### to set ball scale, change factor ]0.0 - 1.0]
+### in 'setattr m ballScale <factor> #0' below,
+### or use the \chimeraballScale{factor} command
+############################################################
+setattr m ballScale 1.0 #0
+
+############################################################
+### display alpha-carbons only
+############################################################
+represent bs @ca; show @ca
+
+############################################################
+### name structure model
+############################################################
+setattr m name logo #0
+
+############################################################
+### logo data
+############################################################
+setattr a radius 1.473 #0:7@ca
+setattr a color #0CC010570517 #0:7@ca
+setattr a name '|| .FLS' #0:7@ca
+setattr a radius 1.061 #0:8@ca
+setattr a color #22962541099F #0:8@ca
+setattr a name '|| .WYLF' #0:8@ca
+setattr a radius 2.096 #0:9@ca
+setattr a color #09032F7DC2EF #0:9@ca
+setattr a name '|| R.KQ' #0:9@ca
+setattr a radius 2.178 #0:10@ca
+setattr a color #CA40C889AC09 #0:10@ca
+setattr a name '|| A.EKQ' #0:10@ca
+setattr a radius 1.232 #0:11@ca
+setattr a color #8A718A714538 #0:11@ca
+setattr a name '|| .VGAYLF' #0:11@ca
+setattr a radius 1.913 #0:12@ca
+setattr a color #09F109F105D4 #0:12@ca
+setattr a name '|| .ILFV' #0:12@ca
+setattr a radius 3.112 #0:13@ca
+setattr a color #FC8DFC8DCC2F #0:13@ca
+setattr a name '|| A:.GSV' #0:13@ca
+setattr a radius 4.322 #0:14@ca
+setattr a color #FFFF00000000 #0:14@ca
+setattr a name '|| E>:.' #0:14@ca
+setattr a radius 3.440 #0:15@ca
+setattr a color #016B016B0083 #0:15@ca
+setattr a name '|| F:.LC' #0:15@ca
+setattr a radius 2.230 #0:16@ca
+setattr a color #075807A505D3 #0:16@ca
+setattr a name '|| .LIVF' #0:16@ca
+setattr a radius 2.657 #0:17@ca
+setattr a color #FFFFFFFF783D #0:17@ca
+setattr a name '|| A.GS' #0:17@ca
+setattr a radius 3.773 #0:18@ca
+setattr a color #D7E8D7E80000 #0:18@ca
+setattr a name '|| T>:.M' #0:18@ca
+setattr a radius 2.097 #0:19@ca
+setattr a color #088A088A0420 #0:19@ca
+setattr a name '|| .LFA' #0:19@ca
+setattr a radius 2.481 #0:20@ca
+setattr a color #00F200F200BD #0:20@ca
+setattr a name '|| L.IFVW' #0:20@ca
+setattr a radius 3.057 #0:21@ca
+setattr a color #004A004A000E #0:21@ca
+setattr a name '|| F.L' #0:21@ca
+setattr a radius 2.701 #0:22@ca
+setattr a color #3BC23BC23BC2 #0:22@ca
+setattr a name '|| V.LI' #0:22@ca
+setattr a radius 2.024 #0:23@ca
+setattr a color #1ECB1ECB069F #0:23@ca
+setattr a name '|| .FYLV' #0:23@ca
+setattr a radius 1.768 #0:24@ca
+setattr a color #1B441B441476 #0:24@ca
+setattr a name '|| .IFALV' #0:24@ca
+setattr a radius 2.841 #0:25@ca
+setattr a color #FFFFFFFF08A6 #0:25@ca
+setattr a name '|| G.TS' #0:25@ca
+setattr a radius 1.326 #0:26@ca
+setattr a color #879582864490 #0:26@ca
+setattr a name '|| .VILC' #0:26@ca
+setattr a radius 2.916 #0:27@ca
+setattr a color #9F8A9F8A175B #0:27@ca
+setattr a name '|| G.LA' #0:27@ca
+setattr a radius 2.371 #0:28@ca
+setattr a color #EF03EF032197 #0:28@ca
+setattr a name '|| S.TAVC' #0:28@ca
+setattr a radius 2.180 #0:29@ca
+setattr a color #E860E860B33C #0:29@ca
+setattr a name '|| V.AGC' #0:29@ca
+setattr a radius 1.761 #0:30@ca
+setattr a color #1CBC1CBC1779 #0:30@ca
+setattr a name '|| .IMALV' #0:30@ca
+setattr a radius 1.470 #0:31@ca
+setattr a color #C42ECDFE4527 #0:31@ca
+setattr a name '|| .GAQN' #0:31@ca
+setattr a radius 1.181 #0:32@ca
+setattr a color #5DEA64CE3980 #0:32@ca
+setattr a name '|| .VYFWA' #0:32@ca
+setattr a radius 0.902 #0:33@ca
+setattr a color #75B6A8AB46D8 #0:33@ca
+setattr a name '|| .KNV' #0:33@ca
+setattr a radius 0.889 #0:34@ca
+setattr a color #10BD5883373D #0:34@ca
+setattr a name '|| .KLR' #0:34@ca
+setattr a radius 0.906 #0:35@ca
+setattr a color #74E177B12C96 #0:35@ca
+setattr a name '|| .SLA' #0:35@ca
+setattr a radius 0.623 #0:36@ca
+setattr a color #83EF89E63287 #0:36@ca
+setattr a name '|| .T' #0:36@ca
+setattr a radius 0.820 #0:37@ca
+setattr a color #D292B0543AE0 #0:37@ca
+setattr a name '|| .SA' #0:37@ca
+setattr a radius 0.623 #0:38@ca
+setattr a color #925787241E9C #0:38@ca
+setattr a name '|| .S' #0:38@ca
+setattr a radius 0.436 #0:39@ca
+setattr a color #4EE56E191F33 #0:39@ca
+setattr a name '|| .' #0:39@ca
+setattr a radius 0.550 #0:40@ca
+setattr a color #B86FC42D53F3 #0:40@ca
+setattr a name '|| .GA' #0:40@ca
+setattr a radius 0.420 #0:41@ca
+setattr a color #19491949024C #0:41@ca
+setattr a name '|| .W' #0:41@ca
+setattr a radius 0.498 #0:42@ca
+setattr a color #01D201360000 #0:42@ca
+setattr a name '|| .LI' #0:42@ca
+setattr a radius 0.312 #0:43@ca
+setattr a color #CCB5A5D24091 #0:43@ca
+setattr a name '|| .' #0:43@ca
+setattr a radius 2.906 #0:44@ca
+setattr a color #1B971B971B0A #0:44@ca
+setattr a name '|| I.VA' #0:44@ca
+setattr a radius 2.647 #0:45@ca
+setattr a color #FC87FC87A050 #0:45@ca
+setattr a name '|| A.SN' #0:45@ca
+setattr a radius 1.815 #0:46@ca
+setattr a color #04BD04BD0447 #0:46@ca
+setattr a name '|| .LWIVF' #0:46@ca
+setattr a radius 2.362 #0:47@ca
+setattr a color #E816E81695BC #0:47@ca
+setattr a name '|| A.GCST' #0:47@ca
+setattr a radius 2.672 #0:48@ca
+setattr a color #006602D30BD3 #0:48@ca
+setattr a name '|| F.HW' #0:48@ca
+setattr a radius 3.512 #0:49@ca
+setattr a color #FFFFFFFF284F #0:49@ca
+setattr a name '|| G:.A' #0:49@ca
+setattr a radius 2.212 #0:50@ca
+setattr a color #142D142D00F9 #0:50@ca
+setattr a name '|| .LGFI' #0:50@ca
+setattr a radius 2.009 #0:51@ca
+setattr a color #8C0F8C0F44B5 #0:51@ca
+setattr a name '|| .AMGS' #0:51@ca
+setattr a radius 2.611 #0:52@ca
+setattr a color #1CAF1CAF1AFA #0:52@ca
+setattr a name '|| I.VL' #0:52@ca
+setattr a radius 1.862 #0:53@ca
+setattr a color #329F329F1E62 #0:53@ca
+setattr a name '|| .FAGMTL' #0:53@ca
+setattr a radius 1.664 #0:54@ca
+setattr a color #760E760E49F7 #0:54@ca
+setattr a name '|| .VTAMILF' #0:54@ca
+setattr a radius 1.938 #0:55@ca
+setattr a color #3AB33AB324F0 #0:55@ca
+setattr a name '|| .LAGM' #0:55@ca
+setattr a radius 2.923 #0:56@ca
+setattr a color #A74DA74DA74D #0:56@ca
+setattr a name '|| V.IA' #0:56@ca
+setattr a radius 1.937 #0:57@ca
+setattr a color #BBE9C06E0F4D #0:57@ca
+setattr a name '|| .YQSAL' #0:57@ca
+setattr a radius 1.734 #0:58@ca
+setattr a color #BF91BF91517A #0:58@ca
+setattr a name '|| .CAVSIT' #0:58@ca
+setattr a radius 1.519 #0:59@ca
+setattr a color #94C794C73679 #0:59@ca
+setattr a name '|| .TAVLGFS' #0:59@ca
+setattr a radius 2.729 #0:60@ca
+setattr a color #E1A0E1A074F3 #0:60@ca
+setattr a name '|| AG.' #0:60@ca
+setattr a radius 1.939 #0:61@ca
+setattr a color #7125B8920DDC #0:61@ca
+setattr a name '|| .GHN' #0:61@ca
+setattr a radius 2.932 #0:62@ca
+setattr a color #102110210EDC #0:62@ca
+setattr a name '|| I.VL' #0:62@ca
+setattr a radius 4.044 #0:63@ca
+setattr a color #F914F91401AF #0:63@ca
+setattr a name '|| S>:.' #0:63@ca
+setattr a radius 0.728 #0:64@ca
+setattr a color #FFFFFFFF20B3 #0:64@ca
+setattr a name '|| .G' #0:64@ca
+setattr a radius 3.132 #0:65@ca
+setattr a color #FFFFFFFF5555 #0:65@ca
+setattr a name '|| GA.' #0:65@ca
+setattr a radius 3.981 #0:66@ca
+setattr a color #06F10C37FAC9 #0:66@ca
+setattr a name '|| H>:.A' #0:66@ca
+setattr a radius 2.420 #0:67@ca
+setattr a color #06C906C906C9 #0:67@ca
+setattr a name '|| I.LVF' #0:67@ca
+setattr a radius 4.322 #0:68@ca
+setattr a color #FFFFFFFF0000 #0:68@ca
+setattr a name '|| N>:.' #0:68@ca
+setattr a radius 4.218 #0:69@ca
+setattr a color #FFFFFFFFFFFF #0:69@ca
+setattr a name '|| P>:.' #0:69@ca
+setattr a radius 4.264 #0:70@ca
+setattr a color #FFFFFFFFFE41 #0:70@ca
+setattr a name '|| A>:.' #0:70@ca
+setattr a radius 3.811 #0:71@ca
+setattr a color #DB83DB83DB83 #0:71@ca
+setattr a name '|| V>:.I' #0:71@ca
+setattr a radius 3.595 #0:72@ca
+setattr a color #FFFFFFFF01B5 #0:72@ca
+setattr a name '|| T:.S' #0:72@ca
+setattr a radius 2.524 #0:73@ca
+setattr a color #03D603D603A0 #0:73@ca
+setattr a name '|| F.LIV' #0:73@ca
+setattr a radius 2.925 #0:74@ca
+setattr a color #EF21EF214BCA #0:74@ca
+setattr a name '|| G.A' #0:74@ca
+setattr a radius 2.254 #0:75@ca
+setattr a color #0D920D920731 #0:75@ca
+setattr a name '|| L.MAFC' #0:75@ca
+setattr a radius 1.789 #0:76@ca
+setattr a color #2518251817DB #0:76@ca
+setattr a name '|| .FLACW' #0:76@ca
+setattr a radius 1.947 #0:77@ca
+setattr a color #226A230D1A05 #0:77@ca
+setattr a name '|| .LVI' #0:77@ca
+setattr a radius 1.627 #0:78@ca
+setattr a color #B633B9314FD0 #0:78@ca
+setattr a name '|| .AGSF' #0:78@ca
+setattr a radius 2.199 #0:79@ca
+setattr a color #50ACA8551176 #0:79@ca
+setattr a name '|| .GRCAS' #0:79@ca
+setattr a radius 1.325 #0:80@ca
+setattr a color #17719FE59351 #0:80@ca
+setattr a name '|| .KRQHN' #0:80@ca
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+setattr a name '|| .' #0:281@ca
+%</AQPlogo>
+% \end{macrocode}
+% \begin{macrocode}
+%<*AQPsublogo>
+############################################################
+###
+### . O ¡ o STRUCTURE MEME ¡ . O o
+###
+### Chimera command file generated from TeXshade logo data
+### use '.cmd' or '.com' suffix
+###
+### Reference sequence: 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8
+###
+############################################################
+
+############################################################
+### residue colors: (set with \memeRed{residues} etc.)
+### DE (Red)
+### HKR (Blue)
+### CGNQSTY (Yellow)
+### FILMW (Black)
+### APV (White)
+############################################################
+
+############################################################
+### residues in labels: (\memelabelcutoff{bit-value})
+### 0.1 bit required to appear
+### > : . indicate 3, 2, and 1 bit levels
+############################################################
+
+############################################################
+### initialize & load structure
+############################################################
+close session; background solid white;
+echo load structure file for 'gi|537250|gb|AAA21363.1|', e.g. PDB 1FX8
+open #0; ~ribbon; ~surface
+
+############################################################
+### to set ball scale, change factor ]0.0 - 1.0]
+### in 'setattr m ballScale <factor> #0' below,
+### or use the \chimeraballScale{factor} command
+############################################################
+setattr m ballScale 1.0 #0
+
+############################################################
+### display alpha-carbons only
+############################################################
+represent bs @ca; show @ca
+
+############################################################
+### duplicate structure;
+### to alter direction or Angstrom distance, set
+### 'move <x, y, or z> 1 <distance> models #1' below,
+### or use the \chimeraaxisdistance{x}{y}{z} command
+############################################################
+combine #0
+move x 1 40 models #1
+
+############################################################
+### focus view and name structure models
+############################################################
+wait; focus #0#1
+setattr m name subfamily #0
+setattr m name remaining #1
+
+############################################################
+### logo data
+############################################################
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+setattr a color #FFFFD379011C #0:272@ca
+setattr a name '|| .N' #0:272@ca
+setattr a radius 0.228 #1:272@ca
+setattr a color #D13FE7828A03 #1:272@ca
+setattr a name '|| .P' #1:272@ca
+setattr a radius 0.191 #0:273@ca
+setattr a color #C60EA7676FFF #0:273@ca
+setattr a name '|| .' #0:273@ca
+setattr a radius 0.194 #1:273@ca
+setattr a color #9CD39CD30000 #1:273@ca
+setattr a name '|| .' #1:273@ca
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+setattr a color #613689B83A54 #0:274@ca
+setattr a name '|| .' #0:274@ca
+setattr a radius 0.322 #1:274@ca
+setattr a color #2BF82BF82BF8 #1:274@ca
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+setattr a radius 0.255 #0:275@ca
+setattr a color #1DCE28090000 #0:275@ca
+setattr a name '|| .L' #0:275@ca
+setattr a radius 0.258 #1:275@ca
+setattr a color #F302E9E9E9E9 #1:275@ca
+setattr a name '|| .PV' #1:275@ca
+setattr a radius 0.182 #0:276@ca
+setattr a color #A4BD906E67CF #0:276@ca
+setattr a name '|| .' #0:276@ca
+setattr a radius 0.184 #1:276@ca
+setattr a color #016802D0F167 #1:276@ca
+setattr a name '|| .' #1:276@ca
+setattr a radius 0.281 #0:277@ca
+setattr a color #AB458B625775 #0:277@ca
+setattr a name '|| .E' #0:277@ca
+setattr a radius 0.284 #1:277@ca
+setattr a color #F2BAF2BAD271 #1:277@ca
+setattr a name '|| .V' #1:277@ca
+setattr a radius 0.255 #0:278@ca
+setattr a color #1FE932E882B0 #0:278@ca
+setattr a name '|| .K' #0:278@ca
+setattr a radius 0.260 #1:278@ca
+setattr a color #232123210000 #1:278@ca
+setattr a name '|| .I' #1:278@ca
+setattr a radius 0.205 #0:279@ca
+setattr a color #519792A45FEC #0:279@ca
+setattr a name '|| .' #0:279@ca
+setattr a radius 0.209 #1:279@ca
+setattr a color #F4FD00000000 #1:279@ca
+setattr a name '|| .D' #1:279@ca
+setattr a radius 0.204 #0:280@ca
+setattr a color #4A097FFF5B9B #0:280@ca
+setattr a name '|| .' #0:280@ca
+setattr a radius 0.202 #1:280@ca
+setattr a color #43B843B847BE #1:280@ca
+setattr a name '|| .' #1:280@ca
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+setattr a color #11C61D553638 #0:281@ca
+setattr a name '|| .L' #0:281@ca
+setattr a radius 0.289 #1:281@ca
+setattr a color #B50400000000 #1:281@ca
+setattr a name '|| .D' #1:281@ca
+%</AQPsublogo>
+% \end{macrocode}
+% \begin{macrocode}
%<*Standard>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
diff --git a/macros/latex/contrib/texshade/texshade.ins b/macros/latex/contrib/texshade/texshade.ins
index 73f08c8f6d..c29495fa68 100644
--- a/macros/latex/contrib/texshade/texshade.ins
+++ b/macros/latex/contrib/texshade/texshade.ins
@@ -1,7 +1,7 @@
%%
%% docstrip install file for texshade.sty
%%
-%% Copyright 1999-2011 Eric Beitz
+%% Copyright 1999-2021 Eric Beitz
%%
\def\batchfile{texshade.ins}
@@ -14,7 +14,7 @@
LaTeX package for typesetting nucleotide and peptide alignments
-Copyright (C) 1999-2011 Eric Beitz
+Copyright (C) 1999-2021 Eric Beitz
See the file texshade.txt
\endpreamble
@@ -32,6 +32,8 @@ See the file texshade.txt
\file{AQP_HMM.sgl}{\from{texshade.dtx}{AQPHMMsgl}}
\file{AQP_HMM.ext}{\from{texshade.dtx}{AQPHMMext}}
\file{AQP_TC.asc}{\from{texshade.dtx}{TCoffee}}
+ \file{AQP_sequence_logo_1FX8.cmd}{\from{texshade.dtx}{AQPlogo}}
+ \file{AQP_subfamily_logo_1FX8.cmd}{\from{texshade.dtx}{AQPsublogo}}
\file{standard.cod}{\from{texshade.dtx}{Standard}}
\file{ciliate.cod}{\from{texshade.dtx}{Ciliate}}}
diff --git a/macros/latex/contrib/texshade/texshade.pdf b/macros/latex/contrib/texshade/texshade.pdf
index f423a08595..53941cff68 100644
--- a/macros/latex/contrib/texshade/texshade.pdf
+++ b/macros/latex/contrib/texshade/texshade.pdf
Binary files differ
diff --git a/macros/latex/contrib/texshade/tsfaq.pdf b/macros/latex/contrib/texshade/tsfaq.pdf
deleted file mode 100644
index 53b9b89528..0000000000
--- a/macros/latex/contrib/texshade/tsfaq.pdf
+++ /dev/null
Binary files differ
diff --git a/macros/latex/contrib/texshade/tsfaq.tex b/macros/latex/contrib/texshade/tsfaq.tex
deleted file mode 100644
index 0ab7a0ec37..0000000000
--- a/macros/latex/contrib/texshade/tsfaq.tex
+++ /dev/null
@@ -1,432 +0,0 @@
-\documentclass[12pt]{article}
-
-
-\begin{document}
-
-
-\noindent
-Eric Beitz \hfill March 2005
-
-\section*{\TeX{}shade: frequently asked questions }
-\bigskip
-
-This is the sixth update of the FAQ list for \TeX{}shade. Feel free to
-contact me if you have problems, questions or suggestions about the
-package. I will post them and provide hopefully helpful hints in
-future issues of this list.
-\bigskip
-
-\noindent
-\qquad email: \texttt{eric.beitz@uni-tuebingen.de}
-\smallskip
-
-\noindent
-\TeX{}shade:
-\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html}
-
-
-\subsection*{A. Increasing \TeX{}'s memory settings}
-\medskip
-
- If you are using \TeX{}shade to align several large sequences (about 1000
- residues/sequence), LaTeX will probably stop compiling and quit with one
- of the following messages:
- \texttt{!\ TeX capacity exceeded, sorry [main memory size=384000]} or
- \texttt{!\ TeX capacity exceeded, sorry [stack size=300]}.
-
-Due to several requests I want to start a list of protocols how
-to increase the standard \TeX{} memory settings for bigger
-alignments. Please contribute to this list by sending me the
-procedure for your particular system.
-
-\begin{enumerate}
-
- \item
-
- \textbf{Oz\TeX{} 4.0 for the Macintosh:}
-
- Find the file `OzTeX:TeX:Configs:Default'. This file contains
- all memory settings. Look for the section
- `\% TeX parameters' and increase the values that \TeX{} complains
- about during the run. You will have to restart Oz\TeX{} before the
- changes are active.
-
- For older versions of Oz\TeX{} the configuration file has the
- same name but the path is somewhat different.
-
-
- \item
-
- \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn)
-
- Find the file: `/usr/share/texmf/web2c/texmf.cnf' or
-
- use \verb|locate texmf.cnf| at the command prompt to find it.
-
- Login as super user. Backup `texmf.cnf' in case you destroy something and
- then open the `texmf.cnf' file in your favorite text editor and use its
- search function to locate \verb|main_memory|. This variable is set to 384000.
- Change this to some higher value, i.e. 4000000 (works fine for me!). The
- total amount of memory should not exceed 8000000, so check the other
- values in that section.
-
- Next, you want to change the stack size. Search for \verb|stack_size|. This
- will be set to 300. I changed it to 4000 and it works fine.
-
- There might be complains by \TeX{} about further specific parameters such
- as \verb|stack_size|. You find all those in the same file.
-
- After this you have to run `texconfig init'.
-
- Logout as root.
-
- After this all should be set for large alignments. Happy \TeX{}ing!
-
- The information on how to achieve this was derived from a mail in the
- te\TeX{} mail archive. The original question was posted by Pascal Francq and
- answered by Rolf Nieprasch.
-
-
- \item
-
- \textbf{MiK\TeX{} for Windows:}
-
- The MiK\TeX{} documentation describes very detailed how the memory
- settings can be changed. In brief, you must locate the
- configuration file `miktex/config/miktex.ini'. In the [MiKTeX]
- section of this file you find all the parameters you need, e.\,g.\
- \verb|mem_min|, \verb|mem_max|, \verb|buf_size|, \verb|stack_size| etc.
-
- It appears, that the standard settings of MiK\TeX{} are bigger
- than that of other \TeX{} installations, so it may not always be necessary
- to increase the values.
-
-
-\end{enumerate}
-
-
-\subsection*{B. Problems using \TeX{}shade}
-\medskip
-
-\begin{enumerate}
-
- \item
-
- \textbf{I cannot \TeX{} the manual because I get the error
- message `\texttt{!\ TeX capacity exceeded, sorry \ldots}'.}
-
- \TeX{}shade needs a lot of memory for setting and shading
- alignments. The manual is a good test for your memory settings
- because it uses many alignments and fingerprints, which are
- in particular memory consuming. If you do not know how to increase
- \TeX's memory settings, and you do not know a \TeX{} wizard either, then
- visit the \TeX{}shade homepage at
- \texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} for
- downloading the manual in either of three formats: DVI, PDF or
- PostScript.
-
-
- \item
-
- \textbf{I can set my alignment only when I reduce the number of
- base-pairs by about 11,000. Otherwise I get the `\texttt{!\ TeX
- capacity exceeded, sorry \ldots}' error.}
-
- There are several parameters defining \TeX's
- usable space. If you are a \TeX{} wizard (or you know one)
- increase the values that
- \TeX{}shade complains about during the run in order to set
- bigger alignments. But do not be disappointed when your \TeX{}
- system will not set an alignment containing thousands of residues.
- There is definitely an upper limit (probably the new \LaTeX3 will
- allow you to use even more memory). Setting alignments is a big job for a
- typesetting system!
-
-
- \item
-
- \textbf{I want to align 80 sequences but I get the
- `\texttt{!\ No room for a new count}' message.}
-
- For each sequence two counter variables are used by \TeX{}shade,
- further 14 counters for other purposes are needed (and \TeX{}
- can handle only 255 counters). This limits the amount of sequences
- to about 100 in theory. But \LaTeX{} itself and each of
- the loaded packages allocates more counters further reducing the maximum
- number of sequences.
-
-
- \item
-
- \textbf{I receive error messages `\texttt{!\ Missing \$ inserted}'
- when \TeX{}ing my alignment. What is wrong?}
-
- At least one of the sequence names in the alignment file contains an
- underscore `\_' symbol. This makes \TeX{} to believe you missed to
- enter math mode because subscript initiated by an underscore is
- only allowed in math. You need to change the sequence name(s) either in the
- alignment file using the `find \& replace' option of your editor or
- by using the \verb|\nameseq| command in the \TeX{}shade environment.
- Nevertheless, subscript and superscript are permitted in sequence names,
- e.\,g. \verb|\nameseq{1}{Name$_{sub}^{super}$}| will result in
- Name$_{sub}^{super}$.
-
- Since v1.3b \TeX{}shade{} is much more tolerant concering special
- characters. Get it and read the section about sequence names.
-
-
- \item
-
- \textbf{My sequence names start out with a number in the
- alignment file. Why are they ignored by \TeX{}shade?}
-
- \TeX{}shade analyzes the first character of each line in the
- alignment file in order to decide whether it is a comment, a
- ruler or a sequence line etc. All lines starting out with a
- non-letter character are interpreted as non-sequence lines. Hence,
- you have to change those names in the alignment file. If you
- want to have sequence names starting with a number you can
- use the \verb|\nameseq| command in the \TeX{}shade environment to
- introduce the number, e.\,g. \verb|\nameseq{1}{57th sequence}|.
-
-
- \item
-
- \textbf{Only a fraction of the residues which are supposed to be
- shaded actually are. Why?}
-
- Make sure that \TeX{}shade knows when protein sequences are to be
- set. Align\-ments in the ALN-format do not contain information about the
- sequence type (DNA or protein). In such cases DNA sequences are
- assumed by \TeX{}shade leading to a shading of only A's, C's, G's,
- R's, T's and Y's. A simple solution is to say \verb|\seqtype{P}| in the
- \verb|texshade| environment.
-
-
- \item
-
- \textbf{Functional shading does not work and I get an error message. Why?}
-
- Same problem as discussed in the point before this one. Functional
- shading is permitted only on protein sequences. So, tell \TeX{}shade
- that you are using a protein alignment.
-
-
- \item
-
- \textbf{There is an incompatiblity between \TeX{}shade (v1.2)
- and the multi-language package `\texttt{babel}'!}
-
- You are right! The command \verb|\language| is defined in both
- packages which leads to error messages. This bug is fixed since
- the release of \TeX{}shade version 1.3 from March 2000. In this
- version \verb|\language| is replaced by two commands:
- \verb|\germanlanguage| and \verb|\englishlanguage|.
-
- \item
-
- \textbf{\TeX{}shade crashes when dashes ``-'' are used as gap
- symbols in alignment input files.}
-
- Yes. Be careful with all kinds of characters that are ``active''
- in \TeX{}, such as \verb|$ _ ^ & % " \|. The dash is not really active
- but two or three consecutive dashes are amalgamated to one longer
- dash in \TeX. Having those characters in an input file might result
- in unforeseen errors or even crashes.
-
- \item
-
- \textbf{I have problems using PHD predictions in \TeX{}shade. An
- empty \texttt{.top} or \texttt{.sec} file is created.}
-
- When you do the PHD run do not restrict the calculation to either
- secondary structure or topology prediction. Turn on everything.
- Otherwise the output will have some ambiguous lines which can not
- be interpreted by \TeX{}shade. Result is an empty
- \texttt{.top} or \texttt{.sec} file.
-
-\end{enumerate}
-
-
-
-\subsection*{C. Changing the output}
-\medskip
-
-\begin{enumerate}
-
- \item
-
- \textbf{How can I force \TeX{}shade to print more residues per line?}
-
- Use the \verb|\residuesperline*| command with the `\verb|*|' extension.
- This will allow you to set any number of residues per line that is
- desired, e.\,g. \verb|\residuesperline*{97}|. But then expect numerous
- `\texttt{!\ Overfull hbox}' errors due to printing lines that
- are broader than the preset \verb|\textwidth|. The same command
- without the `\verb|*|' will calculate the highest number of residues
- fitting in one line and round it to be divisible by five.
-
-
- \item
-
- \textbf{Is it possible to add a caption to the \TeX{}shade output?}
-
- Yes, it is. Since \TeX{}shade v1.5 the \verb|\showcaption|
- command is
- available to add captions on the top or the bottom of the
- alignment. The caption behaves exactly as a figure caption
- including the style, numbering and appearance in the list of
- figures.
- \medskip
-
- Example: \verb|\showcaption{Nice alignment!}|.
-
-
- \item
-
- \textbf{I want a short version of the caption for the `List of
- Figures'. Is this possible?}
-
- Yes, with \TeX{}shade v1.9 short captions have been introduced.
- In addition to \verb|showcaption| use the command
- \verb|shortcaption{|\emph{text}\verb|}|.
- \medskip
-
- Example: \verb|\showcaption{Nice alignment!}|\
- \verb|\shortcaption{Nice}|.
-
-
- \item
-
- \textbf{My alignment file contains the letters `B' and `Z' for
- Asx and Glx, respectively. How can I apply a special shading for
- these?}
-
- Use \verb|\funcgroup| to define `B' and `Z' as functional groups
- and assign the colors and the printing style, e.\,g.
- \medskip
-
- \verb|\funcgroup{B}{White}{Blue}{upper}{up}|
- \smallskip
-
- \verb|\funcgroup{Z}{White}{Red}{upper}{up}|
- \medskip
-
- or add the new residues to an existing group, e.\,g.
- \medskip
-
- \verb|\funcgroup{acidic/amide}{DENQBZ}{Black}{Green}{upper}{up}|.
-
-
- \item
-
- \textbf{How can I build a legend using the `\texttt{shadebox}'
- command?}
-
- The \verb|\shadebox| command simply prints a color-filled box at
- the very location it occurs in the text. This means you have to
- use \verb|\shadebox| in the normal text after the \TeX{}shade environment
- or inside the caption. You find a minimal example below:
- \medskip
-
- \qquad\vbox{%
- \verb|\begin{texshade}{alignmentfile.MSF}|
- \medskip
-
- \qquad \verb|\showcpation{Red box: \shadebox{Red}}|
- \medskip
-
- \qquad \emph{further commands, if needed}
- \medskip
-
- \verb|\end{texshade}|
- }
-
- \medskip
-
- Legend:
-
- \qquad\verb|\shadebox{conserved}|: conserved residues
-
- \qquad\verb|\shadebox{White}|: boring residues
-
- \qquad\verb|\shadebox{Red}|: exciting residues
-
-
-
- \item
-
- \textbf{I do not like the spacing between the feature lines. How
- can I change it?}
-
- Employ the respective space controlling command from the
- following list \verb|\ttopspace|,
- \verb|\topspace|, \verb|\bottomspace|, \verb|\bbottomspace|.
- Those are available since \TeX{}shade v1.5 (see manual).
-
-
-
- \item
-
- \textbf{How can I change gap and match symbols in diverse mode?}
-
- Since \TeX{}shade version 1.7, standard definitions for \verb|diverse|
- mode are:
-
- \begin{verbatim}
- \nomatchresidues{Black}{White}{lower}{up}
- \similarresidues{Black}{White}{lower}{up}
- \conservedresidues{Black}{White}{{.}}{up}
- \allmatchresidues{Black}{White}{{.}}{up}
- \gapchar{-}
- \end{verbatim}
-
- After calling \verb|\shadingmode{diverse}| these commands can be
- used to redefine the \verb|diverse| mode settings (mind the double
- curly braces around the dot-symbol!).
-
-
-
- \item
-
- \textbf{I want to rotate the alignment on the page. Is this possible?}
-
- Yes. Stefan Vogt has found this solution: use pdflscape.sty and
- activate it in the preamble with \verb|\usepackage{pdflscape}|. Then
- put your \TeX{}shade environment inside a \verb|landscape|-environment.
- You also need to adjust the number of residues per line with
- \verb|\residuesperline*{number}| to make them fill the rotated page.
- \medskip
-
- \qquad\vbox{%
- \verb|\begin{landscape}|
-
- \verb|\centering|
-
- \qquad \verb|\begin{texshade}{alignmentfile.MSF}|
-
- \qquad \verb|\residuesperline*{|\emph{number}\verb|}|
- \medskip
-
- \qquad \qquad \emph{further commands, if needed}
- \medskip
-
- \qquad \verb|\end{texshade}|
-
- \verb|\end{landscape}|
- }
-
-
-
- \item
-
- \textbf{I want use the \TeX{}shade and \TeX{}topo logos in my text. How?}
-
- Use the commands: \verb|\TeXshade| and \verb|\TeXtopo|.
-
-
-\end{enumerate}
-
-
-
-\end{document} \ No newline at end of file