texlive[58789] Master/texmf-dist: texshade (7apr21)
commits+preining at tug.org
commits+preining at tug.org
Wed Apr 7 17:07:12 CEST 2021
Revision: 58789
http://tug.org/svn/texlive?view=revision&revision=58789
Author: preining
Date: 2021-04-07 17:07:12 +0200 (Wed, 07 Apr 2021)
Log Message:
-----------
texshade (7apr21)
Modified Paths:
--------------
trunk/Master/texmf-dist/doc/latex/texshade/README
trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
trunk/Master/texmf-dist/source/latex/texshade/texshade.ins
trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
Added Paths:
-----------
trunk/Master/texmf-dist/doc/latex/texshade/AQP_sequence_logo_1FX8.cmd
trunk/Master/texmf-dist/doc/latex/texshade/AQP_subfamily_logo_1FX8.cmd
Removed Paths:
-------------
trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf
trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.tex
Added: trunk/Master/texmf-dist/doc/latex/texshade/AQP_sequence_logo_1FX8.cmd
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/AQP_sequence_logo_1FX8.cmd (rev 0)
+++ trunk/Master/texmf-dist/doc/latex/texshade/AQP_sequence_logo_1FX8.cmd 2021-04-07 15:07:12 UTC (rev 58789)
@@ -0,0 +1,879 @@
+
+############################################################
+###
+### . O \xA1 o STRUCTURE MEME \xA1 . 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
+############################################################
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Property changes on: trunk/Master/texmf-dist/doc/latex/texshade/AQP_sequence_logo_1FX8.cmd
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
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Added: trunk/Master/texmf-dist/doc/latex/texshade/AQP_subfamily_logo_1FX8.cmd
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/AQP_subfamily_logo_1FX8.cmd (rev 0)
+++ trunk/Master/texmf-dist/doc/latex/texshade/AQP_subfamily_logo_1FX8.cmd 2021-04-07 15:07:12 UTC (rev 58789)
@@ -0,0 +1,1715 @@
+
+############################################################
+###
+### . O \xA1 o STRUCTURE MEME \xA1 . 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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Property changes on: trunk/Master/texmf-dist/doc/latex/texshade/AQP_subfamily_logo_1FX8.cmd
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/Master/texmf-dist/doc/latex/texshade/README
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/README 2021-04-07 15:02:50 UTC (rev 58788)
+++ trunk/Master/texmf-dist/doc/latex/texshade/README 2021-04-07 15:07:12 UTC (rev 58789)
@@ -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 at 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)
Modified: trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
===================================================================
(Binary files differ)
Deleted: trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf
===================================================================
(Binary files differ)
Deleted: trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.tex
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.tex 2021-04-07 15:02:50 UTC (rev 58788)
+++ trunk/Master/texmf-dist/doc/latex/texshade/tsfaq.tex 2021-04-07 15:07:12 UTC (rev 58789)
@@ -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 at 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
Modified: trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
===================================================================
--- trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2021-04-07 15:02:50 UTC (rev 58788)
+++ trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2021-04-07 15:07:12 UTC (rev 58789)
@@ -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
@@ -393,16 +393,29 @@
% 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'.
+% }
%
%
%
+%
% \CharacterTable
% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
@@ -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}
@@ -518,7 +535,23 @@
%
%
% \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}
@@ -1950,9 +1984,23 @@
% \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|.
%
%
+%
+%
% \subsection{Customization of the alignment output}
%
% Extensive possibilities are given to the user to customize
@@ -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}|}|
@@ -5795,7 +5894,51 @@
% \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}
%
% \textbf{Appearance of the sequence lines}
@@ -6159,8 +6302,8 @@
%
% \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 at rtfile
+\newwrite\exp at rt@chimerafile
\expandafter\ifx\csname blacktriangleright\endcsname\relax
\openin\structurefile = amssymb.sty
@@ -7104,8 +7248,18 @@
\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}
\expandafter\xdef\csname consC?\endcsname{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 at fshadetrue}
\def\get at 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 at count\the\loopcount\endcsname{\the\res at count}
+ \ifnum\loopcount=\chimera at seqnum \xdef\chimera at stack{\chimera at stack \the\res at count,} \fi
\ifnum\loopcount=\exp at rt@num \xdef\sixth@{\the\res at count}\xdef\seventh@{y}\fi
\ifnum\loopcount=\rule at num\relax
\expandafter\ifnum\csname res at count\rule at num\endcsname>\rule at tens
@@ -17041,6 +17215,7 @@
\the\innerloopcount}
\else
\ifnum\loopcount=\rule at num \xdef\ruler@{\ruler@ -} \fi
+ \ifnum\loopcount=\chimera at seqnum \xdef\chimera at stack{\chimera at stack &,} \fi
\ifx\collect at valtop\yes
\ifnum\v at lseqtop=\loopcount
\xdef\v at ltop{\v at ltop,N}
@@ -19324,9 +19499,628 @@
\divide\loopcount by 100 %
\xdef\third@{\the\loopcount}%
}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\chimeraballScale#1{\xdef\chimerab at llSc@le{#1}}
+\def\chimeraballscale#1{\xdef\chimerab at llSc@le{#1}}
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera at xdist@nce{#1}\xdef\chimera at ydist@nce{#2}\xdef\chimera at zdist@nce{#3}}
+\def\memelabelcutoff#1{%
+ \xdef\label at threshold@lower{#1}
+ \setlength\temp@@length{1000sp}
+ \setlength\temp@@length{\label at threshold@lower\temp@@length}
+ \loopcount=\temp@@length
+ \xdef\label at threshold@lowerIOOO{\the\loopcount}
+ \xdef\label at threshold@lowerremainingIOOO{-\the\loopcount}
+}
+\def\chimera at color@get#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers at nd
+ \else
+ \ifnum`#1>96 \make at upper\fi
+ \if\second@ O \else \expandafter\xdef\csname chimera at col@\first@\endcsname{\second@} \fi
+ \expandafter\chimera at color@get\third@
+ \fi
+}
+\def\memered#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{red}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeblue#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{blue}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeyellow#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{yellow}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeblack#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{black}
+ \expandafter\chimera at color@get\third@
+}
+\def\memewhite#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{white}
+ \expandafter\chimera at color@get\third@
+}
+\def\memenone#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{none}
+ \expandafter\chimera at 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 at colors#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers at nd
+ \else
+ \xdef\second@{\csname chimera at col@\first@\endcsname}
+ \expandafter\xdef\csname chimera at list@\second@\endcsname{\csname chimera at list@\second@\endcsname \first@}
+ \expandafter\chimera at colors\third@
+ \fi
+}
+\def\memeStandardcolors{%
+ \xdef\chimera at col@A{white}
+ \xdef\chimera at col@B{none}
+ \xdef\chimera at col@C{yellow}
+ \xdef\chimera at col@D{red}
+ \xdef\chimera at col@E{red}
+ \xdef\chimera at col@F{black}
+ \xdef\chimera at col@G{yellow}
+ \xdef\chimera at col@H{blue}
+ \xdef\chimera at col@I{black}
+ \xdef\chimera at col@J{none}
+ \xdef\chimera at col@K{blue}
+ \xdef\chimera at col@L{black}
+ \xdef\chimera at col@M{black}
+ \xdef\chimera at col@N{yellow}
+ \xdef\chimera at col@O{none}
+ \xdef\chimera at col@P{white}
+ \xdef\chimera at col@Q{yellow}
+ \xdef\chimera at col@R{blue}
+ \xdef\chimera at col@S{yellow}
+ \xdef\chimera at col@T{yellow}
+ \xdef\chimera at col@U{none}
+ \xdef\chimera at col@V{white}
+ \xdef\chimera at col@W{black}
+ \xdef\chimera at col@X{none}
+ \xdef\chimera at col@Y{yellow}
+ \xdef\chimera at col@Z{none}
+}
+\def\echostructurefile#1{\xdef\echo at filename{, e.g. #1}}
+\def\chimerachain#1{\xdef\chimerach at in{.#1}}
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12
+\newcommand{\structurememe}[2][chimera.cmd]{%
+ \ifx\exp at rt@chimera\n@
+ \xdef\first@{"2 @} \expandafter\check at letter\first@
+ \xdef\first@{"2} \ifletter \get at name@number \fi
+ \xdef\chimera at seqnum{\first@}
+ \xdef\exp at rt@chimera{y}
+ \xdef\first@{"1}
+ \immediate\openout\exp at rt@chimerafile = \first@
+ \fi
+}
+\def\init at chimera@file{%
+ \xdef\chimera at list@red{} \xdef\chimera at list@blue{} \xdef\chimera at list@yellow{} \xdef\chimera at list@black{} \xdef\chimera at list@white{}
+ \xdef\chimera at list@none{}
+ \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
+ \expandafter\chimera at colors\first@
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O \xA1 o STRUCTURE MEME \xA1 . O o}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera at seqnum\endcsname'\echo at filename}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@red \unexpanded{ }(Red)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@blue \unexpanded{ }(Blue)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@yellow \unexpanded{ }(Yellow)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@black \unexpanded{ }(Black)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@white \unexpanded{ }(White)}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label at threshold@lower\unexpanded{ }bit required to appear}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{close session; background solid white;}
+ \immediate\write\exp at rt@chimerafile{echo load structure file for '\csname newseqname\chimera at seqnum\endcsname'\echo at filename}
+ \immediate\write\exp at rt@chimerafile{open #0; ~ribbon; ~surface}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{setattr m ballScale \chimerab at llSc@le \unexpanded{ }#0}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{represent bs @ca; show @ca}
+ \immediate\write\exp at rt@chimerafile{}
+ \ifshow at sublogo
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{combine #0}
+ \ifnum\chimera at xdist@nce>0
+ \immediate\write\exp at rt@chimerafile{move x 1 \chimera at xdist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera at ydist@nce>0
+ \immediate\write\exp at rt@chimerafile{move y 1 \chimera at ydist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera at zdist@nce>0
+ \immediate\write\exp at rt@chimerafile{move z 1 \chimera at zdist@nce \unexpanded{ }models #1}
+ \fi
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{wait; focus #0#1}
+ \ifx\sublogo at name@user\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name subfamily #0}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\sublogo at name@user' \unexpanded{ }#0}
+ \fi
+ \xdef\first@{\sublogo at name@neg &}
+ \ifx\first@\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name remaining #1}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\sublogo at name@neg' \unexpanded{ }#1}
+ \fi
+ \else
+ \immediate\write\exp at rt@chimerafile{\string ############################################################}
+ \immediate\write\exp at rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
+ \immediate\write\exp at rt@chimerafile{\string ############################################################}
+ \ifx\logo at name@user\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name logo #0}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\logo at name@user' \unexpanded{ }#0}
+ \fi
+ \fi
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+}
+\def\make at 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 at chimera@data{%
+ \ifnum\temp at count>0 \else\temp at count=1\relax\temp@@count=0\fi%
+ \loopcount=\temp at count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal at A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal at B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal at C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal at D\fourth@ \else%
+ \expandafter\decimal at E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=\chimera at subfamily@col at black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp at count%
+ \xdef\chimera at subfamily@col at black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera at subfamily@col at 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 at subfamily@col at blue\relax%
+ \ifnum\chimera at subfamily@col at yellow>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at yellow\relax%
+ \else%
+ \ifnum\chimera at subfamily@col at red>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at yellow{\the\loopcount}%
+ \ifnum\chimera at subfamily@col at blue<\chimera at subfamily@col at yellow\relax%
+ \xdef\chimera at subfamily@col at green{\chimera at subfamily@col at blue}%
+ \else%
+ \xdef\chimera at subfamily@col at green{\chimera at subfamily@col at yellow}%
+ \fi%
+ \loopcount=\chimera at subfamily@col at yellow\relax%
+ \advance\loopcount by -\chimera at subfamily@col at green%
+ \xdef\chimera at subfamily@col at yellow{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \advance\loopcount by -\chimera at subfamily@col at green%
+ \xdef\chimera at subfamily@col at blue{\the\loopcount}%
+ \ifnum\chimera at subfamily@col at blue>0\relax%
+ \ifnum\chimera at subfamily@col at green>0\relax%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at subfamily@col at blue{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at subfamily@col at green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \advance\loopcount by \chimera at subfamily@col at yellow%
+ \xdef\chimera at subfamily@col at green{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \advance\loopcount by \chimera at subfamily@col at yellow%
+ \xdef\chimera at subfamily@col at red{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \ifnum\chimera at subfamily@col at green>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \else%
+ \ifnum\chimera at subfamily@col at red>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at green{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera at subfamily@col at green%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera at subfamily@col at red%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera at labelOne@set\n@%
+ \xdef\chimera at labelOne@set{y}%
+ \xdef\chimera at label@subfamily{.\chimera at label@subfamily}%
+ \fi%
+ \immediate\write\exp at rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a name '|| \chimera at label@subfamily' #0:\chimera at res@num\chimerach at in @ca}%
+ \ifshow at sublogo
+ \ifnum\temp@@count>0 \else\temp@@count=1\fi%
+ \loopcount=\temp@@count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal at A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal at B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal at C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal at D\fourth@ \else%
+ \expandafter\decimal at E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=-\chimera at remaining@col at red\relax%
+ \xdef\chimera at remaining@col at red{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at yellow\relax%
+ \xdef\chimera at remaining@col at yellow{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at blue\relax%
+ \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at white\relax%
+ \xdef\chimera at remaining@col at white{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp at count%
+ \xdef\chimera at remaining@col at black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera at remaining@col at black%
+ \xdef\temp@@{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \ifnum\chimera at remaining@col at yellow>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at yellow\relax%
+ \else%
+ \ifnum\chimera at remaining@col at red>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at yellow{\the\loopcount}%
+ \ifnum\chimera at remaining@col at blue<\chimera at remaining@col at yellow\relax%
+ \xdef\chimera at remaining@col at green{\chimera at remaining@col at blue}%
+ \else%
+ \xdef\chimera at remaining@col at green{\chimera at remaining@col at yellow}%
+ \fi%
+ \loopcount=\chimera at remaining@col at yellow\relax%
+ \advance\loopcount by -\chimera at remaining@col at green%
+ \xdef\chimera at remaining@col at yellow{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \advance\loopcount by -\chimera at remaining@col at green%
+ \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \ifnum\chimera at remaining@col at blue>0\relax%
+ \ifnum\chimera at remaining@col at green>0\relax%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at remaining@col at green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \advance\loopcount by \chimera at remaining@col at yellow%
+ \xdef\chimera at remaining@col at green{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \advance\loopcount by \chimera at remaining@col at yellow%
+ \xdef\chimera at remaining@col at red{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \ifnum\chimera at remaining@col at green>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \else%
+ \ifnum\chimera at remaining@col at red>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at green{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera at remaining@col at green%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera at remaining@col at red%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera at label@remainingOne at set\n@%
+ \xdef\chimera at label@remainingOne at set{y}%
+ \xdef\chimera at label@remaining{.\chimera at label@remaining}%
+ \fi%
+ \immediate\write\exp at rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a name '|| \chimera at label@remaining' #1:\chimera at res@num\chimerach at in @ca}%
+ \fi%
+}
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13
+\def\get at chimera@res at num#1,#2@{\xdef\chimera at res@num{#1}\xdef\chimera at stack{#2}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines end %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\next at logo#1:#2,#3@{%
\xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
\ifx\first@\ampers at nd%
+ \ifx\exp at rt@chimera\y@%
+ \xdef\chimera at stack{\chimera at stack @}%
+ \expandafter\get at chimera@res at num\chimera at stack%
+ \ifx\chimera at res@num\ampers at nd%
+ \else%
+ \write at chimera@data%
+ \fi%
+ \xdef\chimera at label@subfamily{}%
+ \xdef\chimera at label@remaining{}%
+ \xdef\chimera at subfamily@col at red{0}%
+ \xdef\chimera at subfamily@col at blue{0}%
+ \xdef\chimera at subfamily@col at yellow{0}%
+ \xdef\chimera at subfamily@col at black{0}%
+ \xdef\chimera at subfamily@col at white{0}%
+ \xdef\chimera at remaining@col at red{0}%
+ \xdef\chimera at remaining@col at blue{0}%
+ \xdef\chimera at remaining@col at yellow{0}%
+ \xdef\chimera at remaining@col at black{0}%
+ \xdef\chimera at remaining@col at white{0}%
+ \xdef\chimera at labelOne@set{n}%
+ \xdef\chimera at labelTwo@set{n}%
+ \xdef\chimera at labelThree@set{n}%
+ \xdef\chimera at label@remainingOne at set{n}%
+ \xdef\chimera at label@remainingTwo at set{n}%
+ \xdef\chimera at label@remainingThree at set{n}%
+ \fi%
\ifx\clear at logo\n@%
\ifx\hide at sig\n@%
\expandafter\firstchar at get\sublogo at sig%
@@ -19348,12 +20142,10 @@
\fi%
\fi%
\temp at count=0%
+ \temp@@count=0%
\kern\box at width%
\advance\outerloopcount by 1 %
\else%
- \ifnum#2=1%
- \temp at count=0%
- \else%
\if\seq at type N%
\loopcount=\second@%
\multiply\loopcount by 2%
@@ -19389,7 +20181,7 @@
\fi\fi\fi\fi%
\xdef\third@{\fl at g\temp@}%
\ifnum\temp at count<0 %
- \ifnum\second@<0 \else\temp at count=0 \fi%
+ \ifnum\second@<0 \else\temp@@count=-\temp at count\relax\temp at count=0 \fi%
\fi%
\ifnum\temp at count>0 %
\loopcount=\temp at count \xdef\fl at g{}%
@@ -19416,7 +20208,64 @@
\kern-\box at width%
\fi%
\advance\temp at count by \second@%
- \fi%
+ \xdef\temp@{\the\temp at count}%
+ \ifx\exp at rt@chimera\y@%
+ \xdef\temp@@{\csname chimera at col@\first@\endcsname}%
+ \ifnum\second@<0 %
+ \xdef\temp@@@{\csname chimera at remaining@col@\temp@@\endcsname}%
+ \temp at count=\temp@@@%
+ \advance\temp at count by \second@%
+ \expandafter\xdef\csname chimera at remaining@col@\temp@@\endcsname{\the\temp at count}%
+ \ifnum\second@<\label at threshold@lowerremainingIOOO%
+ \ifnum\second@<-999%
+ \ifx\chimera at label@remainingOne at set\n@%
+ \xdef\chimera at label@remainingOne at set{y}%
+ \xdef\chimera at label@remaining{.\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-1999%
+ \ifx\chimera at label@remainingTwo at set\n@%
+ \xdef\chimera at label@remainingTwo at set{y}%
+ \xdef\chimera at label@remaining{:\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-2999%
+ \ifx\chimera at label@remainingThree at set\n@%
+ \xdef\chimera at label@remainingThree at set{y}%
+ \xdef\chimera at label@remaining{>\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \xdef\chimera at label@remaining{\first@\chimera at label@remaining}%
+ \fi%
+ \else%
+ \xdef\temp@@@{\csname chimera at subfamily@col@\temp@@\endcsname}%
+ \temp at count=\temp@@@%
+ \advance\temp at count by \second@%
+ \expandafter\xdef\csname chimera at subfamily@col@\temp@@\endcsname{\the\temp at count}%
+ \ifnum\second@>\label at threshold@lowerIOOO%
+ \ifnum\second@>999%
+ \ifx\chimera at labelOne@set\n@%
+ \xdef\chimera at labelOne@set{y}%
+ \xdef\chimera at label@subfamily{.\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>1999%
+ \ifx\chimera at labelTwo@set\n@%
+ \xdef\chimera at labelTwo@set{y}%
+ \xdef\chimera at label@subfamily{:\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>2999%
+ \ifx\chimera at labelThree@set\n@%
+ \xdef\chimera at labelThree@set{y}%
+ \xdef\chimera at label@subfamily{>\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \xdef\chimera at label@subfamily{\first@\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \fi%
+ \temp at count=\temp@%
\fi%
\xdef\temp@{\last at .}%
\ifx\temp@\d at t%
@@ -19926,8 +20775,7 @@
\vspace{-\box at height}%
\vspace{\b at r@stretch\box at height}%
\fi%
-% \vspace{-\bar at length}%%%%%%%%%%%%%%%%%%%%%%%
- \setlength{\bar at length}{0pt}%%%%%%%%%%%%%%%%%%%%%%%
+ \setlength{\bar at length}{0pt}%
\put at feature%
\temp@@count=\b at feature@count%
\advance\temp@@count by 1%
@@ -20680,6 +21528,7 @@
\fi
\ifshow at sublogo \closein\sublogofile \fi
\ifx\exp at rt\y@ \closeout\exp at rtfile \fi
+ \ifx\exp at rt@chimera\y@ \closeout\exp at rt@chimerafile \fi%
\closein\alignfile
\message{)}
}
@@ -20832,8 +21681,6 @@
\ifnum\loopcount<\seq at count \repeat
\xdef\seq at order{\seq at order,@}
\killseq at count=\seq at count
-% \seq at percent=100
-% \ifnum\seq at count>0 \divide\seq at percent by \seq at count \fi
\fi
\fi
}
@@ -21105,6 +21952,14 @@
\xdef\thresh at ld@{\the\loopcount}
\loopcount = \all at thresh@ld \multiply\loopcount by \seq at count \divide\loopcount by 100
\xdef\all at thresh@ld@{\the\loopcount}
+ \if\exp at rt@chimera\y@%
+ \ifshow at logo%
+ \init at chimera@file%
+ \else%
+ \ifshow at sublogo%
+ \init at chimera@file%
+ \fi\fi%
+ \fi%
\bgroup
\ifx\out at put\y@\bigskip\fi
\iffuncmode \show at consfalse \fi
@@ -21262,6 +22117,32 @@
\expandafter\xdef\csname group at num1\endcsname{0}
\expandafter\xdef\csname group at num2\endcsname{0}
\xdef\exp at rt@num{0} \xdef\exp at rt{n}
+\xdef\exp at rt@chimera at num{1} \xdef\exp at rt@chimera{n} \xdef\chimera at stack{}
+\xdef\chimerab at llSc@le{1.0}
+\memelabelcutoff{0.1}
+\xdef\chimera at labelOne@set{n}
+\xdef\chimera at labelTwo@set{n}
+\xdef\chimera at labelThree@set{n}
+\xdef\chimera at labelOne@remaining at set{n}
+\xdef\chimera at labelTwo@remaining at set{n}
+\xdef\chimera at labelThree@remaining at set{n}
+\xdef\chimera at xdist@nce{0} \xdef\chimera at ydist@nce{40} \xdef\chimera at zdist@nce{0}
+\xdef\chimerach at in{} \xdef\chimera at seqnum{0}
+\xdef\chimera at label@subfamily{} \xdef\chimera at label@remaining{}
+\memeStandardcolors
+\xdef\chimera at subfamily@col at red{0}%
+\xdef\chimera at subfamily@col at blue{0}%
+\xdef\chimera at subfamily@col at yellow{0}%
+\xdef\chimera at subfamily@col at black{0}%
+\xdef\chimera at subfamily@col at white{0}%
+\xdef\chimera at subfamily@col at none{0}%
+\xdef\chimera at remaining@col at red{0}%
+\xdef\chimera at remaining@col at blue{0}%
+\xdef\chimera at remaining@col at yellow{0}%
+\xdef\chimera at remaining@col at black{0}%
+\xdef\chimera at remaining@col at white{0}%
+\xdef\chimera at remaining@col at none{0}%
+\xdef\echo at filename{}
\xdef\divref@{0}
\xdef\all at thresh@ld{100} \all at shadefalse
\hidefeaturenames \hidefeaturestylenames
@@ -24118,6 +24999,2606 @@
%</TCoffee>
% \end{macrocode}
% \begin{macrocode}
+%<*AQPlogo>
+############################################################
+###
+### . O \xA1 o STRUCTURE MEME \xA1 . 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 at ca
+setattr a color #0CC010570517 #0:7 at ca
+setattr a name '|| .FLS' #0:7 at ca
+setattr a radius 1.061 #0:8 at ca
+setattr a color #22962541099F #0:8 at ca
+setattr a name '|| .WYLF' #0:8 at ca
+setattr a radius 2.096 #0:9 at ca
+setattr a color #09032F7DC2EF #0:9 at ca
+setattr a name '|| R.KQ' #0:9 at ca
+setattr a radius 2.178 #0:10 at ca
+setattr a color #CA40C889AC09 #0:10 at ca
+setattr a name '|| A.EKQ' #0:10 at ca
+setattr a radius 1.232 #0:11 at ca
+setattr a color #8A718A714538 #0:11 at ca
+setattr a name '|| .VGAYLF' #0:11 at ca
+setattr a radius 1.913 #0:12 at ca
+setattr a color #09F109F105D4 #0:12 at ca
+setattr a name '|| .ILFV' #0:12 at ca
+setattr a radius 3.112 #0:13 at ca
+setattr a color #FC8DFC8DCC2F #0:13 at ca
+setattr a name '|| A:.GSV' #0:13 at ca
+setattr a radius 4.322 #0:14 at ca
+setattr a color #FFFF00000000 #0:14 at ca
+setattr a name '|| E>:.' #0:14 at ca
+setattr a radius 3.440 #0:15 at ca
+setattr a color #016B016B0083 #0:15 at ca
+setattr a name '|| F:.LC' #0:15 at ca
+setattr a radius 2.230 #0:16 at ca
+setattr a color #075807A505D3 #0:16 at ca
+setattr a name '|| .LIVF' #0:16 at ca
+setattr a radius 2.657 #0:17 at ca
+setattr a color #FFFFFFFF783D #0:17 at ca
+setattr a name '|| A.GS' #0:17 at ca
+setattr a radius 3.773 #0:18 at ca
+setattr a color #D7E8D7E80000 #0:18 at ca
+setattr a name '|| T>:.M' #0:18 at ca
+setattr a radius 2.097 #0:19 at ca
+setattr a color #088A088A0420 #0:19 at ca
+setattr a name '|| .LFA' #0:19 at ca
+setattr a radius 2.481 #0:20 at ca
+setattr a color #00F200F200BD #0:20 at ca
+setattr a name '|| L.IFVW' #0:20 at ca
+setattr a radius 3.057 #0:21 at ca
+setattr a color #004A004A000E #0:21 at ca
+setattr a name '|| F.L' #0:21 at ca
+setattr a radius 2.701 #0:22 at ca
+setattr a color #3BC23BC23BC2 #0:22 at ca
+setattr a name '|| V.LI' #0:22 at ca
+setattr a radius 2.024 #0:23 at ca
+setattr a color #1ECB1ECB069F #0:23 at ca
+setattr a name '|| .FYLV' #0:23 at ca
+setattr a radius 1.768 #0:24 at ca
+setattr a color #1B441B441476 #0:24 at ca
+setattr a name '|| .IFALV' #0:24 at ca
+setattr a radius 2.841 #0:25 at ca
+setattr a color #FFFFFFFF08A6 #0:25 at ca
+setattr a name '|| G.TS' #0:25 at ca
+setattr a radius 1.326 #0:26 at ca
+setattr a color #879582864490 #0:26 at ca
+setattr a name '|| .VILC' #0:26 at ca
+setattr a radius 2.916 #0:27 at ca
+setattr a color #9F8A9F8A175B #0:27 at ca
+setattr a name '|| G.LA' #0:27 at ca
+setattr a radius 2.371 #0:28 at ca
+setattr a color #EF03EF032197 #0:28 at ca
+setattr a name '|| S.TAVC' #0:28 at ca
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+setattr a name '|| .' #0:281 at ca
+%</AQPlogo>
+% \end{macrocode}
+% \begin{macrocode}
+%<*AQPsublogo>
+############################################################
+###
+### . O \xA1 o STRUCTURE MEME \xA1 . 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 name '|| .IYVLC' #0:245 at ca
+setattr a radius 1.074 #1:245 at ca
+setattr a color #F152F1529C50 #1:245 at ca
+setattr a name '|| .AG' #1:245 at ca
+setattr a radius 0.719 #0:246 at ca
+setattr a color #931693167451 #0:246 at ca
+setattr a name '|| .VAF' #0:246 at ca
+setattr a radius 0.722 #1:246 at ca
+setattr a color #003F003F0000 #1:246 at ca
+setattr a name '|| .LI' #1:246 at ca
+setattr a radius 2.666 #0:247 at ca
+setattr a color #C231C2310000 #0:247 at ca
+setattr a name '|| G:.LI' #0:247 at ca
+setattr a radius 2.667 #1:247 at ca
+setattr a color #F017F017F017 #1:247 at ca
+setattr a name '|| A:.V' #1:247 at ca
+setattr a radius 0.690 #0:248 at ca
+setattr a color #FFFFFFFFF776 #0:248 at ca
+setattr a name '|| .V' #0:248 at ca
+setattr a radius 0.687 #1:248 at ca
+setattr a color #B671B6719B1F #1:248 at ca
+setattr a name '|| .AW' #1:248 at ca
+setattr a radius 0.549 #0:249 at ca
+setattr a color #5EC05EC01546 #0:249 at ca
+setattr a name '|| .WT' #0:249 at ca
+setattr a radius 0.550 #1:249 at ca
+setattr a color #0AF00AF001D2 #1:249 at ca
+setattr a name '|| .L' #1:249 at ca
+setattr a radius 0.949 #0:250 at ca
+setattr a color #C2E1C2E19C47 #0:250 at ca
+setattr a name '|| .VAF' #0:250 at ca
+setattr a radius 0.956 #1:250 at ca
+setattr a color #B212B2120000 #1:250 at ca
+setattr a name '|| .YL' #1:250 at ca
+setattr a radius 1.218 #0:251 at ca
+setattr a color #6760676014D5 #0:251 at ca
+setattr a name '|| .YF' #0:251 at ca
+setattr a radius 1.218 #1:251 at ca
+setattr a color #00000988AB68 #1:251 at ca
+setattr a name '|| .HW' #1:251 at ca
+setattr a radius 0.459 #0:252 at ca
+setattr a color #1F80486B54BB #0:252 at ca
+setattr a name '|| .KL' #0:252 at ca
+setattr a radius 0.457 #1:252 at ca
+setattr a color #D63877200AF8 #1:252 at ca
+setattr a name '|| .QE' #1:252 at ca
+setattr a radius 0.636 #0:253 at ca
+setattr a color #19F630091EDE #0:253 at ca
+setattr a name '|| .LK' #0:253 at ca
+setattr a radius 0.633 #1:253 at ca
+setattr a color #6636604B0000 #1:253 at ca
+setattr a name '|| .YF' #1:253 at ca
+setattr a radius 1.376 #0:254 at ca
+setattr a color #16D616D60C0F #0:254 at ca
+setattr a name '|| .FMATL' #0:254 at ca
+setattr a radius 1.380 #1:254 at ca
+setattr a color #88D388D38B91 #1:254 at ca
+setattr a name '|| .VI' #1:254 at ca
+setattr a radius 1.213 #0:255 at ca
+setattr a color #35C935C91D68 #0:255 at ca
+setattr a name '|| .IVY' #0:255 at ca
+setattr a radius 1.211 #1:255 at ca
+setattr a color #028E030E0080 #1:255 at ca
+setattr a name '|| .LF' #1:255 at ca
+setattr a radius 0.879 #0:256 at ca
+setattr a color #54FA84E50E07 #0:256 at ca
+setattr a name '|| .GK' #0:256 at ca
+setattr a radius 0.877 #1:256 at ca
+setattr a color #046A15B84D86 #1:256 at ca
+setattr a name '|| .RI' #1:256 at ca
+setattr a radius 0.810 #0:257 at ca
+setattr a color #1A9C584C0000 #0:257 at ca
+setattr a name '|| .CRGM' #0:257 at ca
+setattr a radius 0.811 #1:257 at ca
+setattr a color #E4A4C2EAB745 #1:257 at ca
+setattr a name '|| .AP' #1:257 at ca
+setattr a radius 0.658 #0:258 at ca
+setattr a color #18E657ECD0EB #0:258 at ca
+setattr a name '|| .H' #0:258 at ca
+setattr a radius 0.647 #1:258 at ca
+setattr a color #4F04452D13FC #1:258 at ca
+setattr a name '|| .IRD' #1:258 at ca
+setattr a radius 0.299 #0:259 at ca
+setattr a color #036F083F0EE3 #0:259 at ca
+setattr a name '|| .LI' #0:259 at ca
+setattr a radius 0.304 #1:259 at ca
+setattr a color #F4465F09283D #1:259 at ca
+setattr a name '|| .E' #1:259 at ca
+setattr a radius 0.308 #0:260 at ca
+setattr a color #E8B9B6DA7B02 #0:260 at ca
+setattr a name '|| .P' #0:260 at ca
+setattr a radius 0.314 #1:260 at ca
+setattr a color #0000884F0C77 #1:260 at ca
+setattr a name '|| .RN' #1:260 at ca
+setattr a radius 0.171 #0:261 at ca
+setattr a color #BAF1C65B16D5 #0:261 at ca
+setattr a name '|| .' #0:261 at ca
+setattr a radius 0.184 #1:261 at ca
+setattr a color #F37500000000 #1:261 at ca
+setattr a name '|| .E' #1:261 at ca
+setattr a radius 0.183 #0:262 at ca
+setattr a color #816881685259 #0:262 at ca
+setattr a name '|| .' #0:262 at ca
+setattr a radius 0.191 #1:262 at ca
+setattr a color #FB2FFB2FFB2F #1:262 at ca
+setattr a name '|| .P' #1:262 at ca
+setattr a radius 0.175 #0:263 at ca
+setattr a color #99794A072503 #0:263 at ca
+setattr a name '|| .' #0:263 at ca
+setattr a radius 0.183 #1:263 at ca
+setattr a color #FBB2FBB2FBB2 #1:263 at ca
+setattr a name '|| .P' #1:263 at ca
+setattr a radius 0.257 #0:264 at ca
+setattr a color #B329B329527F #0:264 at ca
+setattr a name '|| .' #0:264 at ca
+setattr a radius 0.270 #1:264 at ca
+setattr a color #00000000FCF2 #1:264 at ca
+setattr a name '|| .H' #1:264 at ca
+setattr a radius 0.140 #0:265 at ca
+setattr a color #9C298771263E #0:265 at ca
+setattr a name '|| .' #0:265 at ca
+setattr a radius 0.150 #1:265 at ca
+setattr a color #00000000F248 #1:265 at ca
+setattr a name '|| .H' #1:265 at ca
+setattr a radius 0.114 #0:266 at ca
+setattr a color #3E674C965C30 #0:266 at ca
+setattr a name '|| .' #0:266 at ca
+setattr a radius 0.120 #1:266 at ca
+setattr a color #74C5C11E023E #1:266 at ca
+setattr a name '|| .' #1:266 at ca
+setattr a radius 0.694 #0:267 at ca
+setattr a color #7FC616752E21 #0:267 at ca
+setattr a name '|| .EDK' #0:267 at ca
+setattr a radius 0.691 #1:267 at ca
+setattr a color #F340F3408FC9 #1:267 at ca
+setattr a name '|| .PAT' #1:267 at ca
+setattr a radius 0.559 #0:268 at ca
+setattr a color #FFFFB29A7B30 #0:268 at ca
+setattr a name '|| .AE' #0:268 at ca
+setattr a radius 0.560 #1:268 at ca
+setattr a color #000023FC3B8A #1:268 at ca
+setattr a name '|| .FH' #1:268 at ca
+setattr a radius 0.707 #0:269 at ca
+setattr a color #8536492225DF #0:269 at ca
+setattr a name '|| .EGA' #0:269 at ca
+setattr a radius 0.703 #1:269 at ca
+setattr a color #25857EE278BF #1:269 at ca
+setattr a name '|| .KTD' #1:269 at ca
+setattr a radius 0.618 #0:270 at ca
+setattr a color #BAEDAA09396E #0:270 at ca
+setattr a name '|| .TV' #0:270 at ca
+setattr a radius 0.613 #1:270 at ca
+setattr a color #AB69B4BC4B4E #1:270 at ca
+setattr a name '|| .SA' #1:270 at ca
+setattr a radius 0.334 #0:271 at ca
+setattr a color #FFFF855C4FB6 #0:271 at ca
+setattr a name '|| .EP' #0:271 at ca
+setattr a radius 0.336 #1:271 at ca
+setattr a color #00B90173E5E0 #1:271 at ca
+setattr a name '|| .K' #1:271 at ca
+setattr a radius 0.230 #0:272 at ca
+setattr a color #FFFFD379011C #0:272 at ca
+setattr a name '|| .N' #0:272 at ca
+setattr a radius 0.228 #1:272 at ca
+setattr a color #D13FE7828A03 #1:272 at ca
+setattr a name '|| .P' #1:272 at ca
+setattr a radius 0.191 #0:273 at ca
+setattr a color #C60EA7676FFF #0:273 at ca
+setattr a name '|| .' #0:273 at ca
+setattr a radius 0.194 #1:273 at ca
+setattr a color #9CD39CD30000 #1:273 at ca
+setattr a name '|| .' #1:273 at ca
+setattr a radius 0.316 #0:274 at ca
+setattr a color #613689B83A54 #0:274 at ca
+setattr a name '|| .' #0:274 at ca
+setattr a radius 0.322 #1:274 at ca
+setattr a color #2BF82BF82BF8 #1:274 at ca
+setattr a name '|| .LV' #1:274 at ca
+setattr a radius 0.255 #0:275 at ca
+setattr a color #1DCE28090000 #0:275 at ca
+setattr a name '|| .L' #0:275 at ca
+setattr a radius 0.258 #1:275 at ca
+setattr a color #F302E9E9E9E9 #1:275 at ca
+setattr a name '|| .PV' #1:275 at ca
+setattr a radius 0.182 #0:276 at ca
+setattr a color #A4BD906E67CF #0:276 at ca
+setattr a name '|| .' #0:276 at ca
+setattr a radius 0.184 #1:276 at ca
+setattr a color #016802D0F167 #1:276 at ca
+setattr a name '|| .' #1:276 at ca
+setattr a radius 0.281 #0:277 at ca
+setattr a color #AB458B625775 #0:277 at ca
+setattr a name '|| .E' #0:277 at ca
+setattr a radius 0.284 #1:277 at ca
+setattr a color #F2BAF2BAD271 #1:277 at ca
+setattr a name '|| .V' #1:277 at ca
+setattr a radius 0.255 #0:278 at ca
+setattr a color #1FE932E882B0 #0:278 at ca
+setattr a name '|| .K' #0:278 at ca
+setattr a radius 0.260 #1:278 at ca
+setattr a color #232123210000 #1:278 at ca
+setattr a name '|| .I' #1:278 at ca
+setattr a radius 0.205 #0:279 at ca
+setattr a color #519792A45FEC #0:279 at ca
+setattr a name '|| .' #0:279 at ca
+setattr a radius 0.209 #1:279 at ca
+setattr a color #F4FD00000000 #1:279 at ca
+setattr a name '|| .D' #1:279 at ca
+setattr a radius 0.204 #0:280 at ca
+setattr a color #4A097FFF5B9B #0:280 at ca
+setattr a name '|| .' #0:280 at ca
+setattr a radius 0.202 #1:280 at ca
+setattr a color #43B843B847BE #1:280 at ca
+setattr a name '|| .' #1:280 at ca
+setattr a radius 0.286 #0:281 at ca
+setattr a color #11C61D553638 #0:281 at ca
+setattr a name '|| .L' #0:281 at ca
+setattr a radius 0.289 #1:281 at ca
+setattr a color #B50400000000 #1:281 at ca
+setattr a name '|| .D' #1:281 at ca
+%</AQPsublogo>
+% \end{macrocode}
+% \begin{macrocode}
%<*Standard>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
Modified: trunk/Master/texmf-dist/source/latex/texshade/texshade.ins
===================================================================
--- trunk/Master/texmf-dist/source/latex/texshade/texshade.ins 2021-04-07 15:02:50 UTC (rev 58788)
+++ trunk/Master/texmf-dist/source/latex/texshade/texshade.ins 2021-04-07 15:07:12 UTC (rev 58789)
@@ -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 @@
\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}}}
Modified: trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
===================================================================
--- trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2021-04-07 15:02:50 UTC (rev 58788)
+++ trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2021-04-07 15:07:12 UTC (rev 58789)
@@ -8,13 +8,13 @@
%%
%% 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
%%
\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}
@@ -56,6 +56,7 @@
\newread\structurefile \newwrite\featurefile
\newread\alignfile \newread\sublogofile
\newwrite\exp at rtfile
+\newwrite\exp at rt@chimerafile
\expandafter\ifx\csname blacktriangleright\endcsname\relax
\openin\structurefile = amssymb.sty
@@ -679,6 +680,16 @@
\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}
\expandafter\xdef\csname consC?\endcsname{0}
@@ -2892,8 +2903,17 @@
\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 at fshadetrue}
\def\get at fromstack#1;#2;#3;#4;#5@{%
@@ -6396,7 +6416,17 @@
\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}
@@ -10443,6 +10473,7 @@
\fi
\fi
\expandafter\xdef\csname res at count\the\loopcount\endcsname{\the\res at count}
+ \ifnum\loopcount=\chimera at seqnum \xdef\chimera at stack{\chimera at stack \the\res at count,} \fi
\ifnum\loopcount=\exp at rt@num \xdef\sixth@{\the\res at count}\xdef\seventh@{y}\fi
\ifnum\loopcount=\rule at num\relax
\expandafter\ifnum\csname res at count\rule at num\endcsname>\rule at tens
@@ -10586,6 +10617,7 @@
\the\innerloopcount}
\else
\ifnum\loopcount=\rule at num \xdef\ruler@{\ruler@ -} \fi
+ \ifnum\loopcount=\chimera at seqnum \xdef\chimera at stack{\chimera at stack &,} \fi
\ifx\collect at valtop\yes
\ifnum\v at lseqtop=\loopcount
\xdef\v at ltop{\v at ltop,N}
@@ -12868,9 +12900,550 @@
\divide\loopcount by 100 %
\xdef\third@{\the\loopcount}%
}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\chimeraballScale#1{\xdef\chimerab at llSc@le{#1}}
+\def\chimeraballscale#1{\xdef\chimerab at llSc@le{#1}}
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera at xdist@nce{#1}\xdef\chimera at ydist@nce{#2}\xdef\chimera at zdist@nce{#3}}
+\def\memelabelcutoff#1{%
+ \xdef\label at threshold@lower{#1}
+ \setlength\temp@@length{1000sp}
+ \setlength\temp@@length{\label at threshold@lower\temp@@length}
+ \loopcount=\temp@@length
+ \xdef\label at threshold@lowerIOOO{\the\loopcount}
+ \xdef\label at threshold@lowerremainingIOOO{-\the\loopcount}
+}
+\def\chimera at color@get#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers at nd
+ \else
+ \ifnum`#1>96 \make at upper\fi
+ \if\second@ O \else \expandafter\xdef\csname chimera at col@\first@\endcsname{\second@} \fi
+ \expandafter\chimera at color@get\third@
+ \fi
+}
+\def\memered#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{red}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeblue#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{blue}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeyellow#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{yellow}
+ \expandafter\chimera at color@get\third@
+}
+\def\memeblack#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{black}
+ \expandafter\chimera at color@get\third@
+}
+\def\memewhite#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{white}
+ \expandafter\chimera at color@get\third@
+}
+\def\memenone#1{%
+ \xdef\third@{#1&@}
+ \xdef\second@{none}
+ \expandafter\chimera at 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 at colors#1#2@{%
+ \xdef\first@{#1}\xdef\third@{#2@}
+ \ifx\first@\ampers at nd
+ \else
+ \xdef\second@{\csname chimera at col@\first@\endcsname}
+ \expandafter\xdef\csname chimera at list@\second@\endcsname{\csname chimera at list@\second@\endcsname \first@}
+ \expandafter\chimera at colors\third@
+ \fi
+}
+\def\memeStandardcolors{%
+ \xdef\chimera at col@A{white}
+ \xdef\chimera at col@B{none}
+ \xdef\chimera at col@C{yellow}
+ \xdef\chimera at col@D{red}
+ \xdef\chimera at col@E{red}
+ \xdef\chimera at col@F{black}
+ \xdef\chimera at col@G{yellow}
+ \xdef\chimera at col@H{blue}
+ \xdef\chimera at col@I{black}
+ \xdef\chimera at col@J{none}
+ \xdef\chimera at col@K{blue}
+ \xdef\chimera at col@L{black}
+ \xdef\chimera at col@M{black}
+ \xdef\chimera at col@N{yellow}
+ \xdef\chimera at col@O{none}
+ \xdef\chimera at col@P{white}
+ \xdef\chimera at col@Q{yellow}
+ \xdef\chimera at col@R{blue}
+ \xdef\chimera at col@S{yellow}
+ \xdef\chimera at col@T{yellow}
+ \xdef\chimera at col@U{none}
+ \xdef\chimera at col@V{white}
+ \xdef\chimera at col@W{black}
+ \xdef\chimera at col@X{none}
+ \xdef\chimera at col@Y{yellow}
+ \xdef\chimera at col@Z{none}
+}
+\def\echostructurefile#1{\xdef\echo at filename{, e.g. #1}}
+\def\chimerachain#1{\xdef\chimerach at in{.#1}}
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12
+\newcommand{\structurememe}[2][chimera.cmd]{%
+ \ifx\exp at rt@chimera\n@
+ \xdef\first@{"2 @} \expandafter\check at letter\first@
+ \xdef\first@{"2} \ifletter \get at name@number \fi
+ \xdef\chimera at seqnum{\first@}
+ \xdef\exp at rt@chimera{y}
+ \xdef\first@{"1}
+ \immediate\openout\exp at rt@chimerafile = \first@
+ \fi
+}
+\def\init at chimera@file{%
+ \xdef\chimera at list@red{} \xdef\chimera at list@blue{} \xdef\chimera at list@yellow{} \xdef\chimera at list@black{} \xdef\chimera at list@white{}
+ \xdef\chimera at list@none{}
+ \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
+ \expandafter\chimera at colors\first@
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O \xA1 o STRUCTURE MEME \xA1 . O o}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera at seqnum\endcsname'\echo at filename}
+ \immediate\write\exp at rt@chimerafile{###}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@red \unexpanded{ }(Red)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@blue \unexpanded{ }(Blue)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@yellow \unexpanded{ }(Yellow)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@black \unexpanded{ }(Black)}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera at list@white \unexpanded{ }(White)}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label at threshold@lower\unexpanded{ }bit required to appear}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{close session; background solid white;}
+ \immediate\write\exp at rt@chimerafile{echo load structure file for '\csname newseqname\chimera at seqnum\endcsname'\echo at filename}
+ \immediate\write\exp at rt@chimerafile{open #0; ~ribbon; ~surface}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{setattr m ballScale \chimerab at llSc@le \unexpanded{ }#0}
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{represent bs @ca; show @ca}
+ \immediate\write\exp at rt@chimerafile{}
+ \ifshow at sublogo
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{combine #0}
+ \ifnum\chimera at xdist@nce>0
+ \immediate\write\exp at rt@chimerafile{move x 1 \chimera at xdist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera at ydist@nce>0
+ \immediate\write\exp at rt@chimerafile{move y 1 \chimera at ydist@nce \unexpanded{ }models #1}
+ \fi
+ \ifnum\chimera at zdist@nce>0
+ \immediate\write\exp at rt@chimerafile{move z 1 \chimera at zdist@nce \unexpanded{ }models #1}
+ \fi
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{wait; focus #0#1}
+ \ifx\sublogo at name@user\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name subfamily #0}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\sublogo at name@user' \unexpanded{ }#0}
+ \fi
+ \xdef\first@{\sublogo at name@neg &}
+ \ifx\first@\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name remaining #1}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\sublogo at name@neg' \unexpanded{ }#1}
+ \fi
+ \else
+ \immediate\write\exp at rt@chimerafile{\string ############################################################}
+ \immediate\write\exp at rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
+ \immediate\write\exp at rt@chimerafile{\string ############################################################}
+ \ifx\logo at name@user\ampers at nd
+ \immediate\write\exp at rt@chimerafile{setattr m name logo #0}
+ \else
+ \immediate\write\exp at rt@chimerafile{setattr m name '\logo at name@user' \unexpanded{ }#0}
+ \fi
+ \fi
+ \immediate\write\exp at rt@chimerafile{}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+ \immediate\write\exp at rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
+ \immediate\write\exp at rt@chimerafile{############################################################}
+}
+\def\make at 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 at chimera@data{%
+ \ifnum\temp at count>0 \else\temp at count=1\relax\temp@@count=0\fi%
+ \loopcount=\temp at count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal at A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal at B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal at C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal at D\fourth@ \else%
+ \expandafter\decimal at E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=\chimera at subfamily@col at black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp at count%
+ \xdef\chimera at subfamily@col at black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera at subfamily@col at black%
+ \xdef\temp@@{\the\loopcount}%
+%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \ifnum\chimera at subfamily@col at yellow>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at yellow\relax%
+ \else%
+ \ifnum\chimera at subfamily@col at red>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at yellow{\the\loopcount}%
+ \ifnum\chimera at subfamily@col at blue<\chimera at subfamily@col at yellow\relax%
+ \xdef\chimera at subfamily@col at green{\chimera at subfamily@col at blue}%
+ \else%
+ \xdef\chimera at subfamily@col at green{\chimera at subfamily@col at yellow}%
+ \fi%
+ \loopcount=\chimera at subfamily@col at yellow\relax%
+ \advance\loopcount by -\chimera at subfamily@col at green%
+ \xdef\chimera at subfamily@col at yellow{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \advance\loopcount by -\chimera at subfamily@col at green%
+ \xdef\chimera at subfamily@col at blue{\the\loopcount}%
+ \ifnum\chimera at subfamily@col at blue>0\relax%
+ \ifnum\chimera at subfamily@col at green>0\relax%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at subfamily@col at blue{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at subfamily@col at green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \advance\loopcount by \chimera at subfamily@col at yellow%
+ \xdef\chimera at subfamily@col at green{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \advance\loopcount by \chimera at subfamily@col at yellow%
+ \xdef\chimera at subfamily@col at red{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue\relax%
+ \ifnum\chimera at subfamily@col at green>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at green\relax%
+ \else%
+ \ifnum\chimera at subfamily@col at red>\loopcount\relax%
+ \loopcount=\chimera at subfamily@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at green{\the\loopcount}%
+ \loopcount=\chimera at subfamily@col at blue%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera at subfamily@col at green%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera at subfamily@col at red%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at subfamily@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera at labelOne@set\n@%
+ \xdef\chimera at labelOne@set{y}%
+ \xdef\chimera at label@subfamily{.\chimera at label@subfamily}%
+ \fi%
+ \immediate\write\exp at rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a name '|| \chimera at label@subfamily' #0:\chimera at res@num\chimerach at in @ca}%
+ \ifshow at sublogo
+ \ifnum\temp@@count>0 \else\temp@@count=1\fi%
+ \loopcount=\temp@@count%
+ \xdef\fourth@{\the\loopcount @}%
+ \ifnum\loopcount>9999 \expandafter\decimal at A\fourth@ \else%
+ \ifnum\loopcount>999 \expandafter\decimal at B\fourth@ \else%
+ \ifnum\loopcount>99 \expandafter\decimal at C\fourth@ \else%
+ \ifnum\loopcount>9 \expandafter\decimal at D\fourth@ \else%
+ \expandafter\decimal at E\fourth@%
+ \fi\fi\fi\fi%
+ \loopcount=-\chimera at remaining@col at red\relax%
+ \xdef\chimera at remaining@col at red{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at yellow\relax%
+ \xdef\chimera at remaining@col at yellow{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at blue\relax%
+ \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at white\relax%
+ \xdef\chimera at remaining@col at white{\the\loopcount}%
+ \loopcount=-\chimera at remaining@col at black%
+ \multiply\loopcount by 65535\relax%
+ \divide\loopcount by \temp at count%
+ \xdef\chimera at remaining@col at black{\the\loopcount}%
+ \loopcount=65535\relax%
+ \advance\loopcount by -\chimera at remaining@col at black%
+ \xdef\temp@@{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \ifnum\chimera at remaining@col at yellow>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at yellow\relax%
+ \else%
+ \ifnum\chimera at remaining@col at red>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at yellow{\the\loopcount}%
+ \ifnum\chimera at remaining@col at blue<\chimera at remaining@col at yellow\relax%
+ \xdef\chimera at remaining@col at green{\chimera at remaining@col at blue}%
+ \else%
+ \xdef\chimera at remaining@col at green{\chimera at remaining@col at yellow}%
+ \fi%
+ \loopcount=\chimera at remaining@col at yellow\relax%
+ \advance\loopcount by -\chimera at remaining@col at green%
+ \xdef\chimera at remaining@col at yellow{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \advance\loopcount by -\chimera at remaining@col at green%
+ \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \ifnum\chimera at remaining@col at blue>0\relax%
+ \ifnum\chimera at remaining@col at green>0\relax%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at remaining@col at blue{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \multiply\loopcount by 2\relax \xdef\chimera at remaining@col at green{\the\loopcount}%
+ \fi%
+ \fi%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \advance\loopcount by \chimera at remaining@col at yellow%
+ \xdef\chimera at remaining@col at green{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \advance\loopcount by \chimera at remaining@col at yellow%
+ \xdef\chimera at remaining@col at red{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue\relax%
+ \ifnum\chimera at remaining@col at green>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at green\relax%
+ \else%
+ \ifnum\chimera at remaining@col at red>\loopcount\relax%
+ \loopcount=\chimera at remaining@col at red\relax%
+ \fi%
+ \fi%
+ \xdef\max at green{\the\loopcount}%
+ \loopcount=\chimera at remaining@col at blue%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@}%
+ \loopcount=\chimera at remaining@col at green%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \loopcount=\chimera at remaining@col at red%
+ \ifnum\max at green>0\relax%
+ \multiply\loopcount by \max at yellow%
+ \divide\loopcount by \max at green%
+ \fi%
+ \advance\loopcount by \chimera at remaining@col at white%
+ \multiply\loopcount by \temp@@%
+ \divide\loopcount by \temp at count%
+ \make at HEX%
+ \xdef\nineth@{\seventh@\nineth@}%
+ \ifx\chimera at label@remainingOne at set\n@%
+ \xdef\chimera at label@remainingOne at set{y}%
+ \xdef\chimera at label@remaining{.\chimera at label@remaining}%
+ \fi%
+ \immediate\write\exp at rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera at res@num\chimerach at in @ca}%
+ \immediate\write\exp at rt@chimerafile{setattr a name '|| \chimera at label@remaining' #1:\chimera at res@num\chimerach at in @ca}%
+ \fi%
+}
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13
+\def\get at chimera@res at num#1,#2@{\xdef\chimera at res@num{#1}\xdef\chimera at stack{#2}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%% Chimera export routines end %%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\next at logo#1:#2,#3@{%
\xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
\ifx\first@\ampers at nd%
+ \ifx\exp at rt@chimera\y@%
+ \xdef\chimera at stack{\chimera at stack @}%
+ \expandafter\get at chimera@res at num\chimera at stack%
+ \ifx\chimera at res@num\ampers at nd%
+ \else%
+ \write at chimera@data%
+ \fi%
+ \xdef\chimera at label@subfamily{}%
+ \xdef\chimera at label@remaining{}%
+ \xdef\chimera at subfamily@col at red{0}%
+ \xdef\chimera at subfamily@col at blue{0}%
+ \xdef\chimera at subfamily@col at yellow{0}%
+ \xdef\chimera at subfamily@col at black{0}%
+ \xdef\chimera at subfamily@col at white{0}%
+ \xdef\chimera at remaining@col at red{0}%
+ \xdef\chimera at remaining@col at blue{0}%
+ \xdef\chimera at remaining@col at yellow{0}%
+ \xdef\chimera at remaining@col at black{0}%
+ \xdef\chimera at remaining@col at white{0}%
+ \xdef\chimera at labelOne@set{n}%
+ \xdef\chimera at labelTwo@set{n}%
+ \xdef\chimera at labelThree@set{n}%
+ \xdef\chimera at label@remainingOne at set{n}%
+ \xdef\chimera at label@remainingTwo at set{n}%
+ \xdef\chimera at label@remainingThree at set{n}%
+ \fi%
\ifx\clear at logo\n@%
\ifx\hide at sig\n@%
\expandafter\firstchar at get\sublogo at sig%
@@ -12892,12 +13465,10 @@
\fi%
\fi%
\temp at count=0%
+ \temp@@count=0%
\kern\box at width%
\advance\outerloopcount by 1 %
\else%
- \ifnum#2=1%
- \temp at count=0%
- \else%
\if\seq at type N%
\loopcount=\second@%
\multiply\loopcount by 2%
@@ -12933,7 +13504,7 @@
\fi\fi\fi\fi%
\xdef\third@{\fl at g\temp@}%
\ifnum\temp at count<0 %
- \ifnum\second@<0 \else\temp at count=0 \fi%
+ \ifnum\second@<0 \else\temp@@count=-\temp at count\relax\temp at count=0 \fi%
\fi%
\ifnum\temp at count>0 %
\loopcount=\temp at count \xdef\fl at g{}%
@@ -12960,7 +13531,64 @@
\kern-\box at width%
\fi%
\advance\temp at count by \second@%
- \fi%
+ \xdef\temp@{\the\temp at count}%
+ \ifx\exp at rt@chimera\y@%
+ \xdef\temp@@{\csname chimera at col@\first@\endcsname}%
+ \ifnum\second@<0 %
+ \xdef\temp@@@{\csname chimera at remaining@col@\temp@@\endcsname}%
+ \temp at count=\temp@@@%
+ \advance\temp at count by \second@%
+ \expandafter\xdef\csname chimera at remaining@col@\temp@@\endcsname{\the\temp at count}%
+ \ifnum\second@<\label at threshold@lowerremainingIOOO%
+ \ifnum\second@<-999%
+ \ifx\chimera at label@remainingOne at set\n@%
+ \xdef\chimera at label@remainingOne at set{y}%
+ \xdef\chimera at label@remaining{.\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-1999%
+ \ifx\chimera at label@remainingTwo at set\n@%
+ \xdef\chimera at label@remainingTwo at set{y}%
+ \xdef\chimera at label@remaining{:\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \ifnum\second@<-2999%
+ \ifx\chimera at label@remainingThree at set\n@%
+ \xdef\chimera at label@remainingThree at set{y}%
+ \xdef\chimera at label@remaining{>\chimera at label@remaining}%
+ \fi%
+ \fi%
+ \xdef\chimera at label@remaining{\first@\chimera at label@remaining}%
+ \fi%
+ \else%
+ \xdef\temp@@@{\csname chimera at subfamily@col@\temp@@\endcsname}%
+ \temp at count=\temp@@@%
+ \advance\temp at count by \second@%
+ \expandafter\xdef\csname chimera at subfamily@col@\temp@@\endcsname{\the\temp at count}%
+ \ifnum\second@>\label at threshold@lowerIOOO%
+ \ifnum\second@>999%
+ \ifx\chimera at labelOne@set\n@%
+ \xdef\chimera at labelOne@set{y}%
+ \xdef\chimera at label@subfamily{.\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>1999%
+ \ifx\chimera at labelTwo@set\n@%
+ \xdef\chimera at labelTwo@set{y}%
+ \xdef\chimera at label@subfamily{:\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \ifnum\second@>2999%
+ \ifx\chimera at labelThree@set\n@%
+ \xdef\chimera at labelThree@set{y}%
+ \xdef\chimera at label@subfamily{>\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \xdef\chimera at label@subfamily{\first@\chimera at label@subfamily}%
+ \fi%
+ \fi%
+ \fi%
+ \temp at count=\temp@%
\fi%
\xdef\temp@{\last at .}%
\ifx\temp@\d at t%
@@ -13470,7 +14098,7 @@
\vspace{-\box at height}%
\vspace{\b at r@stretch\box at height}%
\fi%
- \setlength{\bar at length}{0pt}%%%%%%%%%%%%%%%%%%%%%%%
+ \setlength{\bar at length}{0pt}%
\put at feature%
\temp@@count=\b at feature@count%
\advance\temp@@count by 1%
@@ -13626,10 +14254,10 @@
\fi\fi
\else
\ifnum\code at num=6
- \xdef\second@{\second@\#}
+ \xdef\second@{\second@\#}
\else
\ifnum\code at num=14
- \xdef\second@{\second@\%}
+ \xdef\second@{\second@\%}
\else
\xdef\second@{\second@\noexpand\string\first@}
\fi\fi
@@ -14223,6 +14851,7 @@
\fi
\ifshow at sublogo \closein\sublogofile \fi
\ifx\exp at rt\y@ \closeout\exp at rtfile \fi
+ \ifx\exp at rt@chimera\y@ \closeout\exp at rt@chimerafile \fi%
\closein\alignfile
\message{)}
}
@@ -14645,6 +15274,14 @@
\xdef\thresh at ld@{\the\loopcount}
\loopcount = \all at thresh@ld \multiply\loopcount by \seq at count \divide\loopcount by 100
\xdef\all at thresh@ld@{\the\loopcount}
+ \if\exp at rt@chimera\y@%
+ \ifshow at logo%
+ \init at chimera@file%
+ \else%
+ \ifshow at sublogo%
+ \init at chimera@file%
+ \fi\fi%
+ \fi%
\bgroup
\ifx\out at put\y@\bigskip\fi
\iffuncmode \show at consfalse \fi
@@ -14802,6 +15439,32 @@
\expandafter\xdef\csname group at num1\endcsname{0}
\expandafter\xdef\csname group at num2\endcsname{0}
\xdef\exp at rt@num{0} \xdef\exp at rt{n}
+\xdef\exp at rt@chimera at num{1} \xdef\exp at rt@chimera{n} \xdef\chimera at stack{}
+\xdef\chimerab at llSc@le{1.0}
+\memelabelcutoff{0.1}
+\xdef\chimera at labelOne@set{n}
+\xdef\chimera at labelTwo@set{n}
+\xdef\chimera at labelThree@set{n}
+\xdef\chimera at labelOne@remaining at set{n}
+\xdef\chimera at labelTwo@remaining at set{n}
+\xdef\chimera at labelThree@remaining at set{n}
+\xdef\chimera at xdist@nce{0} \xdef\chimera at ydist@nce{40} \xdef\chimera at zdist@nce{0}
+\xdef\chimerach at in{} \xdef\chimera at seqnum{0}
+\xdef\chimera at label@subfamily{} \xdef\chimera at label@remaining{}
+\memeStandardcolors
+\xdef\chimera at subfamily@col at red{0}%
+\xdef\chimera at subfamily@col at blue{0}%
+\xdef\chimera at subfamily@col at yellow{0}%
+\xdef\chimera at subfamily@col at black{0}%
+\xdef\chimera at subfamily@col at white{0}%
+\xdef\chimera at subfamily@col at none{0}%
+\xdef\chimera at remaining@col at red{0}%
+\xdef\chimera at remaining@col at blue{0}%
+\xdef\chimera at remaining@col at yellow{0}%
+\xdef\chimera at remaining@col at black{0}%
+\xdef\chimera at remaining@col at white{0}%
+\xdef\chimera at remaining@col at none{0}%
+\xdef\echo at filename{}
\xdef\divref@{0}
\xdef\all at thresh@ld{100} \all at shadefalse
\hidefeaturenames \hidefeaturestylenames
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