Math & Science ⇒ Help with TexTopo

[K-Mart]

Dear All,

I'm trying to learn how to use TexTopo, which is a Latex package for displaying the topology of membrane proteins. I'm wondering if anyone has any experience working with this particular package.

I've installed and tried to run the TexTopo package on several different Latex programs (ProText, Texworks, Texmaker) but so far have not been able to reproduce the sample graphics that are given in the TexTopo manual. Here is the link to the TexTopo package:

http://www.uni-kiel.de/pharmazie/chem/P ... extopo.htm

When I try to run following sample command from the TexTopo manual in Texmaker 3.5.2, I get the error message "Can't detect the file name" and "Can't start the command."

Code: Select all

\begin{textopo}
\getsequence{PHD}{AQP1.phd}
\applyshading{similar}{AQPpro.MSF}
\allmatchspecial
\end{textopo}

I would greatly appreciate it if anyone can help.
Thank you very much.

[Johannes_B]

Hi and welcome to the board.

Did you install the package properly via compiling the .ins and .dtx files?


Have you been trying to compile a proper example? Something like:

Code: Select all

\documentclass{scrartcl}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{texshade}
\usepackage{textopo}

\begin{document}

Hello \TeX topo!

\begin{textopo}
\getsequence{PHD}{AQP1.phd}
\applyshading{similar}{AQPpro.MSF}
\allmatchspecial
\end{textopo}

\end{document}

[K-Mart]

Hello Johannes and fellow TexTopo users,

Johannes, when I try to run your sample commands, I get to a point where it's asking me for the following file: tex\latex\koma-script\scrartcl.cls, so I haven't been able to reproduce the graphic in your attached pdf file.

On the other hand, here are some commands that I run and the output that I get. Right now I'm not getting any numbering that I assign (with * around the amino acid) to appear and even though the numbering of the myc tag appears, the myc tag sequence does not. I'm using Texworks editor and TexStudio and both give the same output. Could there be a problem with the conversion to pdf?

Thank you very much for your help.

Code: Select all

\documentclass{article}
\usepackage{textopo}
\begin{document}
\begin{textopo}
\sequence{ MA*T*WDEKAVTRRAKVAPAERMSKFLRHFTVVGDDYHAWNINYKKWENEEEEEEEEQPPPTPVSGEEGRAAAPDVAPAPGPAPRAPLDFRGMLRKLFSSHR[FQVIIICLVVLDALLVLAELILDLK]IIQPDKNNYAA[MVFHYMSITILVFFMMEIIFKLFVF]RLEFFHHKFE[ILDAVVVVVSFILDIVLLF]QEHQFEALG[LLILLRLWRVARIINGIIISV]KTRSERQLLRLKQMNVQLAAKIQHLEFSCSEKEQEIERLNKLLRQHGLLGE*V*N}

\addtagtoNterm[N,8]{MEQKLISEEDAAA}{myc}{myc-tag}
\flipNterm
\loopextent [C] {40 [10]}
\end{textopo}
\end{document}

[K-Mart]

Johannes, I ran your script again and now I'm able to reproduce your file, including the Hello Textopo!
I had to add all extracted TexTopo and TexShade files to my Local Tex files folder that's searched by my
Texworks and then it worked.

Unfortunately, when I ran my script again, I got the same screwed up image as the one that I have attached
in my previous post.

I would greatly appreciate your help on this matter.
Thank you all for any help.

[Johannes_B]

Hi K-Mart,

I never worked with the textopo-package before, and right now I just skimmed the documentation. Concerning the numbering with the asterisks: The Documentation says, the the output is seen on the screen, that means in your case in the logfile. In TexWorks you can see this file in the small part at the bottom of your window, where all error messages appear, too.

Concerning your second problem, I am a little bit confused myself. I don`t have time right now to read the documentation carefully. Maybe do it yourself and try to figure out things for yourself. The myc-tag appears in your pdf, but i cannot confirm if its right aligned. I just don`t know anything about this stuff.

Maybe someone else can help you?


Best regards

[K-Mart]

Hi Johannes,

Thank you very much for looking into the issue.
I greatly appreciate your help.
If I or anyone else comes up with a solution, I'll post it on here.