TeXtopo v1.5 >> >> 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) 2000-2011 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: ebeitz@pharmazie.uni-kiel.de WWW: http://www.pharmazie.uni-kiel.de/chem/ (On-line documentation and updates) Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry, Gutenbergstrasse 76, D-24118 Kiel (Germany) 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.