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TeXtopo v1.4
>>
>> A LaTeX package for shaded membrane protein topology plots.
>>
>> PHD topology predictions are a mighty tool to localize trans-
>> membrane domains and the protruding loops. SwissProt database
>> files provide sequence feature informations, such as mutation
>> sites, important domains, or secondary modifications. Making
>> these data visible in a sophisticated topology plot is an
>> enormous effort when using a standard drawing software.
>>
>> TeXtopo is a LaTeX2e macro package that provides two new envi-
>> ronments: (a) the textopo environment is used for plotting to-
>> pology data of membrane proteins derived from PHD predictions,
>> from SwissProt database files or from manually entered data
>> containing sequence and transmembrane domain information, and
>> (b) the helical wheel environment draws transmembrane domains
>> as seen from above or beneath the cell membrane.
>>
>> Both kinds of plots can be richly decorated with special sha-
>> ding for domains of interest, with labels and legends. TeXtopo
>> is fully compatible with TeXshade (v1.3 and up) -- the compre-
>> hensive alignment shading package for the TeX community. This
>> allows one to apply calculated shading based on sequence con-
>> servation and functional aspects of the residue sidechains.
>>
Copyright (C) 2000-2005 Eric Beitz
FOR THE HASTY READER
Be sure to use a docstrip version 2.4 or later!
Otherwise you will not be able to tex the documentation!
1 - FILES DISTRIBUTED WITH THIS PACKAGE
textopo.ins Batch file, run through LaTeX
textopo.dtx Docstrip archive, run twice through LaTeX
textopo.txt This file
(a) FILES THAT WILL BE GENERATED FROM TEXTOPO.INS
textopo.sty LaTeX package
textopo.def Standard definitions
AQPpro.MSF Example protein alignment file (.MSF-format)
AQPpro1.shd Shading information calculated from AQPpro.MSF
AQP2spec.ALN Example protein alignment file (.ALN-format)
AQP1.phd Example PHD secondary structure file
AQP1.tpo Topology data extracted from AQP1.phd
AQP1.SP SwissProt database file
AQP1.swp Information extracted from AQP1.SP
biotex.sty Style file which organizes the BioTeX Bundle
(b) FILE THAT WILL BE GENERATED FROM TEXTOPO.DTX
textopo.dvi Package documentation
2 - INSTALLATION
(a) EXTRACTING FILES FROM THE DOCSTRIP ARCHIVE
All files provided by TeXtopo are compacted to one single file,
namely "textopo.dtx". To extract the archive run "textopo.ins"
- which contains the corresponding instructions - through LaTeX.
A list of the generated files is given above, see 1(a).
AGAIN: Be sure to use a docstrip version 2.4 or later! Otherwise
you will not be able to tex the documentation!
(b) THE DOCUMENTATION
The file "textopo.dtx" further contains the package documentation.
Therefore, run this file through LaTeX now. As you will recognize
two runs are needed to make proper references within the document.
TeXtopo needs lots of LaTeX's memory, so adjust your parameter set-
tings to make TeXtopo feel comfortable. The documentation is a
good test for this. (If you have problems TeXing the doc, you can
download an on-line version [PDF-, DVI-, or PostScript format] at
http://homepages.uni-tuebingen.de/beitz/)
The resulting file "textopo.dvi" can be viewed and printed using a
DVI-viewer which is able to display embedded PostScript. Another
possibility is to run "textopo.dvi" through DVIPS, a DVI to Post-
Script converter, and finally view and print the converted file
which will be most likely "textopo.ps" with GhostView from the GNU
free software foundation.
TeXtopo makes use of "color.sty" by David Carlisle. This style is
part of the Standard LaTeX Graphics Bundle. Usually, the bundle is
present in a comprehensive LaTeX installation. If this is not the
case for your system you have to download the package from a CTAN-
server, e.g. ftp.dante.de.
(c) MAKING TEXTOPO.STY AVAILABLE FOR YOUR LATEX SYSTEM
In the final step, copy at least the files "textopo.sty" and
"biotex.sty" to a directory searched by TeX in order to make these
files available for all documents you produce in the future. The
remaining files are example files which are not necessary for run-
ning TeXtopo. Nevertheless, it would be a good idea to keep all the
files together.
3 - CONTACT
E-Mail: eric.beitz@uni-tuebingen.de
WWW: http://homepages.uni-tuebingen.de/beitz/
(On-line documentation and updates)
Address: Eric Beitz, Universit"at T"ubingen, Pharmazeutische Chemie,
Auf der Morgenstelle 8, D-72076 T"ubingen (Germany)
4 - AGREEMENT
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 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 General Public License for more details.
In order to receive a copy of the GNU General Public License write to
the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
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