[cmview-devel] CMView application note and testing

[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The official website with the old version and (out of date) manual is: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.