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Hi again Bernhard,
Sorry, I went too fast, I was talking from what I remembered... Now,
that I checked it out, I see that, in fact, in the "Surface/Area Volume"
tool you can only select "Accessible surface (Gerstein)" if you want to
get the full ATOM line for each atom. Then you parse for those lines
having a value in the last column greater than 0 A² (or whatever value
you choose)
grep ATOM filefrom.chimera | awk '{ if ($12 > 0) print $0}' > exposed
I hope this helps,
Miguel
Miguel Ortiz Lombardia wrote:
> Hi Bernhard,
>
> You can use chimera (http://www.cgl.ucsf.edu/chimera/) for that.
>
> Open your pdb, go to:
>
> Tools->Surface/Binding Analysis->Surface/Area Analysis
>
> it will open a dialog window. In the "Chains" tab select the model/chain
> you are interested in. In the "Compute" button you can select betweeen
> accessible, msms, or Voronoi surfaces. Mark either "Save server output
> to file" or "Show server output in browser". In either case, you will be
> given a list of atoms (their lines in your coordinates file plus two
> more columns) from which you can easily parse the B-factors and compute
> that average.
>
> Cheers,
>
>
> Miguel
>
> Bernhard Rupp wrote:
>>> *** For details on how to be removed from this list visit the ***
>>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>>
>>>
>>> Dear All,
>>>
>>> I am trying to find a program/script/procedure that allows me to
>>> get an average B of the surface exposed residues.
>>> Grateful for suggestions.
>>> Thx, br
>>> --------------------------------------------
>>> Bernhard Rupp, FRS
>>> www.ruppweb.org
>>> --------------------------------------------
>>>
>>>
>>>
>
> --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> email: [EMAIL PROTECTED]
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Le travail est ce que l'homme a trouvé de mieux
> pour ne rien faire de sa vie. (Raoul Vaneigem)
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie. (Raoul Vaneigem)
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