for the pymol-users mailing list archive and to close my message
Tsjerk Wassenaar gave the command :
print cmd.count_atoms("byres resn URE within 3.5 of peptide")/8. it works !!!
Thanks to him !!!
Bye
Stephane
------------------------------
Message: 8
Date: Fri, 28 Sep 2012 12:59:27 +0000
From: ABEL Stephane 175950 <[email protected]>
Subject: [PyMOL] Obtain the number of molecule in the first hydration
shell of a peptide.
To: "[email protected]"
<[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="us-ascii"
Dear pymol users,
I would like to obtain with Pymol (v1.3) the number of urea molecules in the
first shell of a peptide. To do this I have defined the object urea as following
select UREA, resn URE
and used the following cutoff for the first hydration shell:
select UREA_firstshell, UREA within 3.5 of peptide
And finally used the command:
print cmd.count_atoms("UREA_firstshell") to obtain the number of atom at the
distance of 3.5 A from the peptide.
Of course, these commands work well, but my aim is to obtain the number of
molecules instead of the number of atoms. How to do that ?
For info, urea has 8 atoms.
Thank you for you help
Stephane
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