[cmview-devel] saving cmaps

[Henning Stehr]

Hi Marika,

you can use the OWL Java library which CMView is based on:
http://www.bioinformatics.org/owl/.
If you check out the code from the SVN repository (instructions are on
the website), you will find a command line tool called "genGraph"
which should do the job. It can generate contact maps for a list of
PDBs in a few different text formats. All of them are line based, i.e.
they contain one contact per line. So if you really need the matrix
format you may need to write a small script to convert them to this
format.

Hope that helps,
Henning


On Sun, Sep 30, 2012 at 9:11 AM, Marika Joanna Ciombor
<179845 at student.pwr.wroc.pl> wrote:
>
> Ok, Thank you. And is it possible to save cmap to a text file (as a matrix 0
> and 1 or column) without opening the interface. If it is impossible, do You
> know a program that does this?
>
> Cheers,
> Ciombor M.
>
> W dniu 26/09/12 Henning Stehr <stehr at molgen.mpg.de> napisał:
>
> Yes, that is possible. The command line option is "-I". This will
> output a PNG image without starting the graphical interface. So a
> typical command line would be:
>
> cmview -f myprotein.pdb -t Cb -d 8.0 -I out.png
>
> You can also use "cmview -h" to see all supported command line options.
>
> Cheers,
> Henning
>
> On Wed, Sep 26, 2012 at 1:30 PM, Marika Joanna Ciombor
> <179845 at student.pwr.wroc.pl> wrote:
>>  Hello,
>>        I would like to ask if CMView can save generated cmaps from pdb
>> file,
>> but without opening the interface. I need to save a lot of cmap and I
>> would
>> like to use the command window on Linux.
>> Regards,
>> Ciombor M.
>>
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