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FAQ

1. Who created CMView?
2. What are the license terms for CMView?
3. How to cite the CMView software?
4. How can I obtain the source code?
5. Is there a mailing list?
6. Haw can I avoid Java out of memory exceptions?
7. Why does the cmview.cfg file not properly display in Windows?
8. Is there a DSSP version for MacOSX?

1.

Who created CMView?

CMView was was originally created by researchers of the Structural Proteomics Group at the Max Planck Institute for Molecular Genetics. It is now maintained by a community of developers working in academia and industry.

2.

What are the license terms for CMView?

CMView is licensed under the GNU General Public License. If you use CMView in published work, we ask you to give proper citation (see below).

3.

How to cite the CMView software?

Please use the following citation:

CMView: Interactive contact map visualization and analysis
Corinna Vehlow; Henning Stehr; Matthias Winkelmann; Jose M. Duarte; Lars Petzold; Juliane Dinse; Michael Lappe
Bioinformatics 2011; doi: 10.1093/bioinformatics/btr163

You can access the paper here: Abstract, PDF.

4.

How can I obtain the source code?

The latest development version can be cloned from the git repository. CMView requires the OWL library which is also available on GitHub.

5.

Is there a mailing list?

There are mailing lists for users and for developers. Please sign up to the users mailing list to be notified of new versions and to ask questions about the usage of CMView.

6.

Haw can I avoid Java out of memory exceptions?

For large proteins the contact map calculation may use more than the preset amount of memory. Try setting the -Xmx parameter in the startup script to a higher value (e.g. -Xmx512m or -Xmx1024m). Alternatively, if CMView does not start because you have limited memory available, you can also set a lower value.

7.

Why does the cmview.cfg file not properly display in Windows?

The file uses Unix-style line terminators wich causes some Windows editors to ignore the line breaks. If you use the Wordpad application instead of Notepad, the file should display properly.

8.

Is there a DSSP version for MacOSX?

The DSSP version for Mac available from http://swift.cmbi.ru.nl/gv/dssp/ is for the classic environment which is not supported anymore by current MacOS versions. However, we were able to successfully compile DSSP for MacOSX from source code using the included make file. The source code is available from the above URL.