General ⇒ Installing Textopo

[6mzp]

Hello all,

I am such a novice at all of this, and am having trouble installing the Textopo program. The instructions say to "run" textopo.ins, and then "run" textopo.dtx, twice, in Latex.

Can someone please tell me how exactly to do this?

I have downloaded TexLive, and the editor seems to be TexWorks.

I would really love to start making some topology diagrams with this software!

Thanks

[nlct]

It seems that textopo is distributed with texlive, so you should be able to get it using texlive's package manager. If not, "run" textopo.ins means open textopo.ins in texworks, make sure the drop down box is set to "pdflatex" (or "latex") and press the green triangle button. This will create the require .sty file(s). Do the same with textopo.dtx, which will create the documentation. Next you need to move the .sty files to somewhere TeX can find them and refresh the TeX database (open a command prompt window and type "texhash" or, if that doesn't work "mktexlsr").

Regards
Nicola Talbot

[6mzp]

So if the textopo.sty file cannot be found, would I get the error message that the "textopo environment is undefined"?

[6mzp]

Thanks for the reply.

do I need to include a "document class" for textopo? If so, what is the class I should use? I placed the textopo.sty file in C:\texlive\2011\texmf-dist\tex\latex\textopo. I think that's the right place? Anyway, when I try running the script

Code: Select all

\documentclass{article}
\usepackage{textopo}
\begin{textopo}
\getsequence{PHD}{AQP1.phd}
\end{textopo}

I get the error message:

Code: Select all

Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(c:/texlive/2011/texmf-dist/tex/latex/base/size10.clo)) (./textopo.sty
! Undefined control sequence.
l.1 \run
         {C:\Documents and Settings\Owner\My Documents\textopo.ins}
? 

Any suggestions?

thanks so much

[nlct]

Code: Select all

\documentclass{article}
    \usepackage{textopo}
    \begin{textopo}
    \getsequence{PHD}{AQP1.phd}
    \end{textopo}

You've missed the document environment. Here's an example that doesn't rely on an external file:

Code: Select all

\documentclass{article}

\usepackage{textopo}

\begin{document}

\begin{textopo}
\sequence{MASEIKKKLFWRAV[VAEFLAMTLFVFISIGSA]LGFNYPLERN
QTLVQDN[VKVSLAFGLSIATLAQSVG]HISGAHSNPAVTL[GLLLSCQISILR
AVMYIIAQCVGAI]VASAILSGITSSLLENSLGRNDLARGVNSG[QGLGIEIIG
TLQLVLCVL]ATTDRRRRDLGGSA[PLAIGLSVALGHLLAIDY]TGCGINPARS
FGSAVLTRNFSNHWI[FWVGPFIGSALAVLIYDFI]LAPRSSDFTDRMKVWTSG
QVEEYDLDADDINSRVMKPK}
\end{textopo}

\end{document}

Code: Select all

Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(c:/texlive/2011/texmf-dist/tex/latex/base/size10.clo)) (./textopo.sty

This is saying that it's picking up textopo.sty from the current directory (the same folder as your document) rather than from C:\texlive\2011\texmf-dist\tex\latex\textopo

Code: Select all

! Undefined control sequence.
l.1 \run
         {C:\Documents and Settings\Owner\My Documents\textopo.ins}
? 

This is very odd. It suggests something's gone wrong with the installation. Try opening textopo.sty with texworks. The start of the file should look something like:

Code: Select all

%%
%% This is file `textopo.sty',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% textopo.dtx  (with options: `textpo')
%% 
%% A LaTeX package for shaded membrane protein topology plots
%% 
%% Copyright (C) 2000-2005 Eric Beitz
%% See the file textopo.txt
%% 
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{textopo}[2001/03/09 LaTeX TeXtopo (v1.4)]

Regards
Nicola Talbot

[6mzp]

Yes, the file looks just like that when I open it. When I run the script you provided I get the following:

Code: Select all

(c:/texlive/2011/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(c:/texlive/2011/texmf-dist/tex/latex/base/size10.clo)) (./textopo.sty
! Undefined control sequence.
l.1 \run
         {C:\Documents and Settings\Owner\My Documents\textopo.ins}
? 

Should I try to reinstall textopo? Does this mean uninstalling what I already tried to install?!!

Thanks again for your help

[nlct]

According to your error message, line 1 of textopo.sty contains:

Code: Select all

\run{C:\Documents and Settings\Owner\My Documents\textopo.ins}

which doesn't make sense. Try deleting the version of textopo.sty that's in the same folder as your document and retry. If that doesn't work, you may have to try reinstalling:

1. Open textopo.ins in texworks
2. Run latex
3. Move textopo.sty to c:/texlive/2011/texmf-dist/tex/latex/textopo/
4. Open the MSDOS command prompt (usually in Accessories)
5. Type texhash or, if that doesn't work, mktexlsr
6. Keep the command prompt open and type

   Code: Select all

   kpsewhich textopo.sty

   This should list the correct location of textopo.sty
7. Retry the sample document

Regards
Nicola Talbot

[6mzp]

Ok, So when I enter the code:

Code: Select all

kpsewhich textopo.sty

I get the response:

./textopo.sty

Where does that mean it is?

Thanks

[6mzp]

I redid all of the steps you suggested and this was the output, again:

Code: Select all

This is pdfTeX, Version 3.1415926-2.3-1.40.12 (Web2C 2011)
 restricted \write18 enabled.
entering extended mode
(./text textopo.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2011-07-01, ngerman-x-2011-07-01, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(c:/texlive/2011/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(c:/texlive/2011/texmf-dist/tex/latex/base/size10.clo)) (./textopo.sty
! Undefined control sequence.
l.1 \run
         {C:\Documents and Settings\Owner\My Documents\textopo.ins}
? 

[6mzp]

Update:

I did a search of all files and folders for "textopo.sty" and it turned up quite a few hits (who knows why), so I deleted them all except the one in texlive\2011\texmf-dist\tex\latex\textopo. That seemed to work because when I re-entered the code you gave I ACTUALLY GOT A TOPOLOGY PLOT!!! This is a big day, so thank you.

Meagan