    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.
