diff options
Diffstat (limited to 'Master/texmf-dist/source/latex')
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.dtx | 3519 | ||||
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.ins | 6 |
2 files changed, 3504 insertions, 21 deletions
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx index adf4e661c36..2f2f4da380a 100644 --- a/Master/texmf-dist/source/latex/texshade/texshade.dtx +++ b/Master/texmf-dist/source/latex/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 +setattr a radius 2.039 #0:81@ca +setattr a color #0B5509E10989 #0:81@ca +setattr a name '|| .ILVFM' #0:81@ca +setattr a radius 2.139 #0:82@ca +setattr a color #EBA3E17B31D8 #0:82@ca +setattr a name '|| S.PT' #0:82@ca +setattr a radius 1.836 #0:83@ca +setattr a color #0885099206BB #0:83@ca +setattr a name '|| .LIWV' #0:83@ca +setattr a radius 1.108 #0:84@ca +setattr a color #257E35D21A7C #0:84@ca +setattr a name '|| .LTIA' #0:84@ca +setattr a radius 2.072 #0:85@ca +setattr a color #09DB2D14C16B #0:85@ca +setattr a name '|| R.KT' #0:85@ca +setattr a radius 1.938 #0:86@ca +setattr a color #B352B3527D7B #0:86@ca +setattr a name '|| .AGVLSF' #0:86@ca +setattr a radius 1.921 #0:87@ca +setattr a color #40DE40DE40DE #0:87@ca +setattr a name '|| .VILPA' #0:87@ca +setattr a radius 1.176 #0:88@ca +setattr a color #2C092D871C5C #0:88@ca +setattr a name '|| .FLPV' #0:88@ca +setattr a radius 3.969 #0:89@ca +setattr a color #EEE0EEE001AE #0:89@ca +setattr a name '|| Y>:.M' #0:89@ca +setattr a radius 2.150 #0:90@ca +setattr a color #093809380797 #0:90@ca +setattr a name '|| .IWMV' #0:90@ca +setattr a radius 2.112 #0:91@ca +setattr a color #463346333E14 #0:91@ca +setattr a name '|| .IVAL' #0:91@ca +setattr a radius 2.760 #0:92@ca +setattr a color #BC20B92EA154 #0:92@ca +setattr a name '|| A.MS' #0:92@ca +setattr a radius 4.322 #0:93@ca +setattr a color #FFFFFFFF0000 #0:93@ca +setattr a name '|| Q>:.' #0:93@ca +setattr a radius 1.979 #0:94@ca +setattr a color #4BD14BD1101F #0:94@ca +setattr a name '|| .CLVIF' #0:94@ca +setattr a radius 2.917 #0:95@ca +setattr a color #09F209F209F2 #0:95@ca +setattr a name '|| L:.VIA' #0:95@ca +setattr a radius 4.045 #0:96@ca +setattr a color #FFFFFFFF0C26 #0:96@ca +setattr a name '|| G>:.A' #0:96@ca +setattr a radius 3.214 #0:97@ca +setattr a color #FFFFFFFFBD68 #0:97@ca +setattr a name '|| A:.SG' #0:97@ca +setattr a radius 2.067 #0:98@ca +setattr a color #106310630AA7 #0:98@ca +setattr a name '|| I.VFMT' #0:98@ca +setattr a radius 1.755 #0:99@ca +setattr a color #89AB89AB53A6 #0:99@ca +setattr a name '|| .CVAIL' #0:99@ca +setattr a radius 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'|| .' #0:261@ca +setattr a radius 0.220 #0:262@ca +setattr a color #A69CA69C854A #0:262@ca +setattr a name '|| .' #0:262@ca +setattr a radius 0.231 #0:263@ca +setattr a color #B9C28208662A #0:263@ca +setattr a name '|| .' #0:263@ca +setattr a radius 0.215 #0:264@ca +setattr a color #A565AD6A4F30 #0:264@ca +setattr a name '|| .' #0:264@ca +setattr a radius 0.120 #0:265@ca +setattr a color #8C0082AA2555 #0:265@ca +setattr a name '|| .' #0:265@ca +setattr a radius 0.133 #0:266@ca +setattr a color #6CD88C653BF1 #0:266@ca +setattr a name '|| .' #0:266@ca +setattr a radius 0.684 #0:267@ca +setattr a color #CCC3A7885B01 #0:267@ca +setattr a name '|| .PA' #0:267@ca +setattr a radius 0.598 #0:268@ca +setattr a color #215145631FCA #0:268@ca +setattr a name '|| .F' #0:268@ca +setattr a radius 0.897 #0:269@ca +setattr a color #3ED96AAF3F60 #0:269@ca +setattr a name '|| .KE' #0:269@ca +setattr a radius 0.771 #0:270@ca +setattr a color #7DFB8C3642F1 #0:270@ca +setattr a name '|| .SLPA' #0:270@ca +setattr a radius 0.412 #0:271@ca +setattr a color #62D273CCB108 #0:271@ca +setattr a name '|| .K' #0:271@ca +setattr a radius 0.237 #0:272@ca +setattr a color #EEB6E6125BD0 #0:272@ca +setattr a name '|| .' #0:272@ca +setattr a radius 0.254 #0:273@ca +setattr a color #CAABA0853237 #0:273@ca +setattr a name '|| .' #0:273@ca +setattr a radius 0.262 #0:274@ca +setattr a color #4A0258CF3B35 #0:274@ca +setattr a name '|| .' #0:274@ca +setattr a radius 0.253 #0:275@ca +setattr a color #841384135601 #0:275@ca +setattr a name '|| .' #0:275@ca +setattr a radius 0.200 #0:276@ca +setattr a color #49027CD3A992 #0:276@ca +setattr a name '|| .' #0:276@ca +setattr a radius 0.300 #0:277@ca +setattr a color #C28EAE1351EB #0:277@ca +setattr a name '|| .' #0:277@ca +setattr a radius 0.264 #0:278@ca +setattr a color #22614CB10DE2 #0:278@ca +setattr a name '|| .' #0:278@ca +setattr a radius 0.288 #0:279@ca +setattr a color #434B36849955 #0:279@ca +setattr a name '|| .K' #0:279@ca +setattr a radius 0.192 #0:280@ca +setattr a color #558E6CE37C71 #0:280@ca +setattr a name '|| .' #0:280@ca +setattr a radius 0.232 #0:281@ca +setattr a color #2E471A71358C #0:281@ca +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 +############################################################ +setattr a radius 1.413 #0:7@ca +setattr a color #017A017A046F #0:7@ca +setattr a name '|| .LWMK' #0:7@ca +setattr a radius 1.408 #1:7@ca +setattr a color #17361752081A #1:7@ca +setattr a name '|| FSA' #1:7@ca +setattr a radius 0.795 #0:8@ca +setattr a color #368759C23733 #0:8@ca +setattr a name '|| .MKVA' #0:8@ca +setattr a radius 0.799 #1:8@ca +setattr a color #26AC26AC0000 #1:8@ca +setattr a name '|| .WY' #1:8@ca +setattr a radius 1.377 #0:9@ca +setattr a color #BB08AF463B97 #0:9@ca +setattr a name '|| .VSGTAN' #0:9@ca +setattr a radius 1.386 #1:9@ca +setattr a color #00000137DFF9 #1:9@ca +setattr a name '|| .RK' #1:9@ca +setattr a radius 2.223 #0:10@ca +setattr a color #A97E52390E6C #0:10@ca +setattr a name '|| .EQKWND' #0:10@ca +setattr a radius 2.225 #1:10@ca +setattr a color #F078F5B6E5FC #1:10@ca +setattr a name '|| A:.' #1:10@ca +setattr a radius 0.931 #0:11@ca +setattr a color #33DA33DA03B6 #0:11@ca +setattr a name '|| .FCT' #0:11@ca +setattr a radius 0.930 #1:11@ca +setattr a color #ABB8ABB867E3 #1:11@ca +setattr a name '|| .VGL' #1:11@ca +setattr a radius 0.906 #0:12@ca +setattr a color #02C102C10000 #0:12@ca +setattr a name '|| .L' #0:12@ca +setattr a radius 0.907 #1:12@ca +setattr a color #51EA51EA37E3 #1:12@ca +setattr a name '|| .IVT' #1:12@ca +setattr a radius 1.929 #0:13@ca +setattr a color #E361E3610000 #0:13@ca +setattr a name '|| .GSTM' #0:13@ca +setattr a radius 1.931 #1:13@ca +setattr a color #F042F042F042 #1:13@ca +setattr a name '|| A.V' #1:13@ca +setattr a radius 0.001 #0:14@ca +setattr a color #FFFF00000000 #0:14@ca +setattr a name '|| .' #0:14@ca +setattr a radius 0.001 #1:14@ca +setattr a color #000000000000 #1:14@ca +setattr a name '|| .' #1:14@ca +setattr a radius 0.947 #0:15@ca +setattr a color #DA0DDA0D2AE9 #0:15@ca +setattr a name '|| .CVTG' #0:15@ca +setattr a radius 0.949 #1:15@ca +setattr a color #000000000000 #1:15@ca +setattr a name '|| .F' #1:15@ca +setattr a radius 1.205 #0:16@ca +setattr a color #008300830000 #0:16@ca +setattr a name '|| L.' #0:16@ca +setattr a radius 1.201 #1:16@ca +setattr a color #23C025AE1D9F #1:16@ca +setattr a name '|| .IV' #1:16@ca +setattr a radius 2.268 #0:17@ca +setattr a color #FFFFFFFF0000 #0:17@ca +setattr a name '|| G:.' #0:17@ca +setattr a radius 2.265 #1:17@ca +setattr a color #FFA8FFA8D161 #1:17@ca +setattr a name '|| A.S' #1:17@ca +setattr a radius 0.610 #0:18@ca +setattr a color #FFFFFFFF0000 #0:18@ca +setattr a name '|| .T' #0:18@ca +setattr a radius 0.610 #1:18@ca +setattr a color #0A3D0A3D0000 #1:18@ca +setattr a name '|| .MS' #1:18@ca +setattr a radius 1.223 #0:19@ca +setattr a color #B26AB26A77B3 #0:19@ca +setattr a name '|| .AMYG' #0:19@ca +setattr a radius 1.224 #1:19@ca +setattr a color #00C100C10000 #1:19@ca +setattr a name '|| .LFI' #1:19@ca +setattr a radius 1.021 #0:20@ca +setattr a color #3F1F3F1F3F1F #0:20@ca +setattr a name '|| .IV' #0:20@ca +setattr a radius 1.016 #1:20@ca +setattr a color #00BA00BA0000 #1:20@ca +setattr a name '|| .LWM' #1:20@ca +setattr a radius 3.234 #0:21@ca +setattr a color #004900490049 #0:21@ca +setattr a name '|| L:.MV' #0:21@ca +setattr a radius 3.235 #1:21@ca +setattr a color #006A006A0000 #1:21@ca +setattr a name '|| F>:.Y' #1:21@ca +setattr a radius 2.123 #0:22@ca +setattr a color #000000000000 #0:22@ca +setattr a name '|| I.M' #0:22@ca +setattr a radius 2.122 #1:22@ca +setattr a color #503B503B503B #1:22@ca +setattr a name '|| V.L' #1:22@ca +setattr a radius 1.631 #0:23@ca +setattr a color #198619861986 #0:23@ca +setattr a name '|| .IVLMA' #0:23@ca +setattr a radius 1.630 #1:23@ca +setattr a color #494249420000 #1:23@ca +setattr a name '|| .YF' #1:23@ca +setattr a radius 1.693 #0:24@ca +setattr a color #005A005A0000 #0:24@ca +setattr a name '|| .FL' #0:24@ca +setattr a radius 1.691 #1:24@ca +setattr a color #47B447B4371E #1:24@ca +setattr a name '|| .IAVG' #1:24@ca +setattr a radius 1.749 #0:25@ca +setattr a color #FFFFFFFF0000 #0:25@ca +setattr a name '|| G.' #0:25@ca +setattr a radius 1.746 #1:25@ca +setattr a color #FF8EFF8E163F #1:25@ca +setattr a name '|| T.SA' #1:25@ca +setattr a radius 0.938 #0:26@ca +setattr a color #FFFFFFFF26C1 #0:26@ca +setattr a name '|| .NCAGT' #0:26@ca +setattr a radius 0.936 #1:26@ca +setattr a color #849179BF529B #1:26@ca +setattr a name '|| .VIS' #1:26@ca +setattr a radius 1.511 #0:27@ca +setattr a color #FFFFFFFF0000 #0:27@ca +setattr a name '|| G.S' #0:27@ca +setattr a radius 1.507 #1:27@ca +setattr a color #201720172017 #1:27@ca +setattr a name '|| .LAV' #1:27@ca +setattr a radius 1.494 #0:28@ca +setattr a color #FFFFFFFF8BA6 #0:28@ca +setattr a name '|| .VCA' #0:28@ca +setattr a radius 1.496 #1:28@ca +setattr a color #FA8BFA8B0000 #1:28@ca +setattr a name '|| .TS' #1:28@ca +setattr a radius 1.126 #0:29@ca +setattr a color #9E249E24761D #0:29@ca +setattr a name '|| .VIC' #0:29@ca +setattr a radius 1.125 #1:29@ca +setattr a color #FFC4FFC4C29C #1:29@ca +setattr a name '|| .ATG' #1:29@ca +setattr a radius 1.985 #0:30@ca +setattr a color #FFFFFFFFF274 #0:30@ca +setattr a name '|| A.' #0:30@ca +setattr a radius 1.980 #1:30@ca +setattr a color #055E055E033D #1:30@ca +setattr a name '|| .IMLV' #1:30@ca +setattr a radius 0.860 #0:31@ca +setattr a color #73229C7B0000 #0:31@ca +setattr a name '|| .QHM' #0:31@ca +setattr a radius 0.853 #1:31@ca +setattr a color #90879CBE1EEE #1:31@ca +setattr a name '|| .G' #1:31@ca +setattr a radius 0.902 #0:32@ca +setattr a color #6306630650D8 #0:32@ca +setattr a name '|| .VLMT' #0:32@ca +setattr a radius 0.905 #1:32@ca +setattr a color #2A49355B0000 #1:32@ca +setattr a name '|| .YWF' #1:32@ca +setattr a radius 0.680 #0:33@ca +setattr a color #E7C0CD29A547 #0:33@ca +setattr a name '|| .VT' #0:33@ca +setattr a radius 0.675 #1:33@ca +setattr a color #B909CA8F530E #1:33@ca +setattr a name '|| .ASG' #1:33@ca +setattr a radius 1.038 #0:34@ca +setattr a color #07C807C807C8 #0:34@ca +setattr a name '|| .LV' #0:34@ca +setattr a radius 1.025 #1:34@ca +setattr a color #038A7C8944CB #1:34@ca +setattr a name '|| .KRS' #1:34@ca +setattr a radius 0.578 #0:35@ca +setattr a color #0D49A28B664F #0:35@ca +setattr a name '|| .K' #0:35@ca +setattr a radius 0.576 #1:35@ca +setattr a color #292A184A076A #1:35@ca +setattr a name '|| .L' #1:35@ca +setattr a radius 0.646 #0:36@ca +setattr a color #00008D9294F1 #0:36@ca +setattr a name '|| .KGR' #0:36@ca +setattr a radius 0.640 #1:36@ca +setattr a color #B433A77E4332 #1:36@ca +setattr a name '|| .TP' #1:36@ca +setattr a radius 0.452 #0:37@ca +setattr a color #9ECE9ECE1FAB #0:37@ca +setattr a name '|| .TG' #0:37@ca +setattr a radius 0.450 #1:37@ca +setattr a color #CD8F816D2FDB #1:37@ca +setattr a name '|| .DN' #1:37@ca +setattr a radius 0.422 #0:38@ca +setattr a color #0D429CCA926A #0:38@ca +setattr a name '|| .KS' #0:38@ca +setattr a radius 0.418 #1:38@ca +setattr a color #D4E6630C3B33 #1:38@ca +setattr a name '|| .DP' #1:38@ca +setattr a radius 0.356 #0:39@ca +setattr a color #31ED4EDB2A76 #0:39@ca +setattr a name '|| .F' #0:39@ca +setattr a radius 0.356 #1:39@ca +setattr a color #1C6865342C63 #1:39@ca +setattr a name '|| .KT' #1:39@ca +setattr a radius 0.518 #0:40@ca +setattr a color #A11CBD470000 #0:40@ca +setattr a name '|| .G' #0:40@ca +setattr a radius 0.521 #1:40@ca +setattr a color #CCF6CCF6B3D6 #1:40@ca +setattr a name '|| .A' #1:40@ca +setattr a radius 0.325 #0:41@ca +setattr a color #406540650587 #0:41@ca +setattr a name '|| .' #0:41@ca +setattr a radius 0.330 #1:41@ca +setattr a color #000000000000 #1:41@ca +setattr a name '|| .W' #1:41@ca +setattr a radius 0.588 #0:42@ca +setattr a color #020001590000 #0:42@ca +setattr a name '|| .LI' #0:42@ca +setattr a radius 0.593 #1:42@ca +setattr a color #000000000000 #1:42@ca +setattr a name '|| .F' #1:42@ca +setattr a radius 0.355 #0:43@ca +setattr a color #D53DA87C33FE #0:43@ca +setattr a name '|| .T' #0:43@ca +setattr a radius 0.364 #1:43@ca +setattr a color #379937993799 #1:43@ca +setattr a name '|| .FA' #1:43@ca +setattr a radius 0.566 #0:44@ca +setattr a color #000000000000 #0:44@ca +setattr a name '|| .IL' #0:44@ca +setattr a radius 0.564 #1:44@ca +setattr a color #FF17FF17F185 #1:44@ca +setattr a name '|| .AVP' #1:44@ca +setattr a radius 1.724 #0:45@ca +setattr a color #FFFFFFFF2A2B #0:45@ca +setattr a name '|| N.TV' #0:45@ca +setattr a radius 1.728 #1:45@ca +setattr a color #F855F855F855 #1:45@ca +setattr a name '|| A.' #1:45@ca +setattr a radius 0.698 #0:46@ca +setattr a color #22F922F9119F #0:46@ca +setattr a name '|| .FA' #0:46@ca +setattr a radius 0.703 #1:46@ca +setattr a color #01CB01CB01CB #1:46@ca +setattr a name '|| .WL' #1:46@ca +setattr a radius 2.055 #0:47@ca +setattr a color #932593250000 #0:47@ca +setattr a name '|| G.IM' #0:47@ca +setattr a radius 2.056 #1:47@ca +setattr a color #F01EF01EBADB #1:47@ca +setattr a name '|| A.CS' #1:47@ca +setattr a radius 2.214 #0:48@ca +setattr a color #079F079F01E5 #0:48@ca +setattr a name '|| W.Y' #0:48@ca +setattr a radius 2.212 #1:48@ca +setattr a color #000002BD253F #1:48@ca +setattr a name '|| F.H' #1:48@ca +setattr a radius 0.626 #0:49@ca +setattr a color #FFFFFFFF0000 #0:49@ca +setattr a name '|| .GS' #0:49@ca +setattr a radius 0.626 #1:49@ca +setattr a color #FFFFFFFFE153 #1:49@ca +setattr a name '|| .A' #1:49@ca +setattr a radius 0.995 #0:50@ca +setattr a color #19D219D20CE9 #0:50@ca +setattr a name '|| .IFVM' #0:50@ca +setattr a radius 0.998 #1:50@ca +setattr a color #CC96CC960000 #1:50@ca +setattr a name '|| .GL' #1:50@ca +setattr a radius 1.489 #0:51@ca +setattr a color #FFFFFFFF6E34 #0:51@ca +setattr a name '|| .GA' #0:51@ca +setattr a radius 1.485 #1:51@ca +setattr a color #31B031B00834 #1:51@ca +setattr a name '|| .MSTV' #1:51@ca +setattr a radius 2.601 #0:52@ca +setattr a color #FFFFFFFFF6F0 #0:52@ca +setattr a name '|| V:.' #0:52@ca +setattr a radius 2.601 #1:52@ca +setattr a color #004400440016 #1:52@ca +setattr a name '|| I.L' #1:52@ca +setattr a radius 1.498 #0:53@ca +setattr a color #8A498A491FA6 #0:53@ca +setattr a name '|| .TMLSV' #0:53@ca +setattr a radius 1.502 #1:53@ca +setattr a color #06AE06AE0000 #1:53@ca +setattr a name '|| F.G' #1:53@ca +setattr a radius 1.328 #0:54@ca +setattr a color #000000000000 #0:54@ca +setattr a name '|| .MLF' #0:54@ca +setattr a radius 1.328 #1:54@ca +setattr a color #E272E2728541 #1:54@ca +setattr a name '|| .TAV' #1:54@ca +setattr a radius 1.775 #0:55@ca +setattr a color #FFFFFFFF7892 #0:55@ca +setattr a name '|| .GAP' #0:55@ca +setattr a radius 1.769 #1:55@ca +setattr a color #024A024A0091 #1:55@ca +setattr a name '|| L.MS' #1:55@ca +setattr a radius 1.021 #0:56@ca +setattr a color #000000000000 #0:56@ca +setattr a name '|| .IL' #0:56@ca +setattr a radius 1.021 #1:56@ca +setattr a color 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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}}} |