Re: [PyMOL] Obtain the number of molecule in the first hydration shell of a peptide.

[Jason V. <jas...@sc...>]

Hi Stephane,

Tsjerk as usual provides a clever answer. However, if in any case a
urea goes missing an atom, maybe due to experimental reasons, or you
want to use this technique for something other than urea then Tsjerk's
answer will need to be modified.

I offer a slightly different solution. I've written a script that
counts distinct molecular objects in a given selection. You can
download it from the PyMOLWiki here,

    http://www.pymolwiki.org/index.php/Count_molecules_in_selection.

See the examples to learn how to use it.

Tsjerk's solution will always be faster. Mine will be more flexible.
Use what works for you.

Cheers,

-- Jason

On Fri, Sep 28, 2012 at 10:03 AM, ABEL Stephane 175950
<Ste...@ce...> wrote:
> 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 <Ste...@ce...>
> Subject: [PyMOL] Obtain the number of molecule in the first hydration
>         shell of a peptide.
> To: "pym...@li..."
>         <pym...@li...>
> Message-ID:
>         <3E39B768BB199548AB18F7289E7534AF02C4D8C0@EXDAG0-B0.intra.cea.fr>
> 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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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120