Hi Stephane,
print cmd.count_atoms("byres resn URE within 3.5 of peptide")/8
Cheers,
Tsjerk
On Fri, Sep 28, 2012 at 2:59 PM, ABEL Stephane 175950
<[email protected]> wrote:
> 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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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
------------------------------------------------------------------------------
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