Thank you for your response, i will try your suggestion
A bientot
Stephane
________________________________________
De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder
[spel...@users.sourceforge.net]
Date d'envoi : jeudi 22 septembre 2011 11:14
À : ABEL Stephane 175950
Cc : pymol-users@lists.sourceforge.net
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a
protein surface
Hi Stephane,
you can select those waters using the "within" or "gap" selection
operators. "within" measures from the atom centre, whereas "gap" takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell, solvent within 3.5 of polymer
# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)
# shows the selected water molecules as a sphere
show spheres, firstshell and elem O
# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print >> stored.out, '## At 0.5 Ang of the protein surface there are',
print >> stored.out, cmd.count_atoms('firstshell and elem O'),
print >> stored.out, 'water molecules'
print >> stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print >> stored.out, ID, resi')
stored.out.close()
python end
http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate
Hope that helps,
Cheers,
Thomas
On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
> Hi All,
>
> I have simulated a protein in water cubic box and I would like to
> know how to show and obtain the number of water in the first shell of
> the protein (or at x Ang of the protein surface) using a pymol
> script. I can to do this using the pymol GUI but I would prefer that
> the script :
>
> - shows the selected water molecules as a sphere
> - and writes the results in a file with the water ID (i.e. residue
> number), for example like this:
>
> ## At x Ang of the protein surface there are XX water molecules
> ## Water ID are
>
> Thanks in advance for your help.
>
> Stephane
--
Thomas Holder
MPI for Developmental Biology
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