[cmview-devel] CMView application note and testing

Henning Stehr stehr at molgen.mpg.de
Tue Dec 14 06:41:02 EST 2010

---------- Forwarded message ----------
From: C. Vehlow <c.vehlow at gmx.de>
Date: Tue, Dec 14, 2010 at 12:17 PM
Subject: Re: [cmview-devel] CMView application note and testing
To: Henning Stehr <stehr at molgen.mpg.de>

Hallo Henning,

also ich habe CMView zum Laufen bekommen, jedoch startet Pymol bei mir nicht:
d:\Downloads\CMView>java -jar CMView-RC1.jar
Starting CMView 1.5.0
Loading configuration file cmview.cfg
Using temporary directory C:\Users\lioness\AppData\Local\Temp\
Connecting to PyMol...
Starting PyMol...
Failed: Cannot run program "D:\Downloads\CMView\PyMOL": CreateProcess error=5, Z
ugriff verweigert

Ich habe es eigentlich auf meiner C:Partition installiert, da sind
dann allerdings Leerzeichen im Pfad und das verursacht Probleme. Ich
habe daher den ganzen Ordner kopiert und es lässt sich von dort aus
auch starten. Nur leider nicht zusammen mit CMView.
Hast du eine Idee?

Ansonsten habe ich bei mir auch schon das erste Problem, welches ich
Freitag beheben muss. Werde dann auch meine Rechner mitbringen um es
parallel wieder zu testen.


Am 10.12.2010 19:11, schrieb Henning Stehr:
> Dear CMView developers,
> in the last few weeks we have been working on an application note
> about CMView which we
> want to submit to Bioinformatics. The paper is almost ready. Now, what we need
> is an updated version of CMView which the reviewers and future readers
> of the paper can
> download and use. Today we have built a version based on the latest
> trunk. Some of the new
> features which we didn't want to make public (mainly because they are
> not stable or
> difficult to explain) have been hidden as "experimental". Still there
> are many changes
> compared to the last version which are not extensively tested (or
> rather hardly tested at all).
> Now we need as many people as possible to test this version and report
> bugs (of which we are
> sure there will be many). Next friday (17/Nov), we will have a
> debugging day so we want to
> collect as many bug reports as possible until then.
> We have set up a Google Docs spreadsheet as a minimal 'bug tracker'
> where you can report everything
> that you notice. You can access the document here:
> https://spreadsheets.google.com/ccc?key=0AtxuyQNfKWkndFdtU0xjTEladVJaYXc0dGtmZllhR1E&hl=en&authkey=CLXwrKUI
> The official website with the old version and (out of date) manual is:
> http://www.bioinformatics.org/cmview/
> Since you are experienced CMView users, here is the very short version
> of the installation instructions for
> the test version:
> 1. Download the file http://www.molgen.mpg.de/~lappe/CMView-RC1.jar
> 2. Download the file http://www.molgen.mpg.de/~lappe/cmview.cfg and
> put it in your home directory
> 3. Download and install PyMol (e.g. from
> http://sourceforge.net/projects/pymol/files/Legacy/)
> 4. Download and install DSSP from http://swift.cmbi.ru.nl/gv/dssp/
> 5. (Optionally) download and install DALI from
> http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/download.html
> 6. Add the paths to PyMol, DSSP and Dali to your cmview.cfg
> 7. Run CMView with java -jar CMView-RC1.jar
> On Windows and Mac it may be enough to doubleclick on the jar file,
> but in any case you need Java 1.6 installed.
> Happy testing!
> Henning
> P.S. Everyone who has contributed to CMView in the past will be an
> author on the paper.
> P.P.S. We were not able to make the build script run so we used
> Eclipse to generate the jar.
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