Bartholomeus,
Your question seems to be essentially the same as one asked on the ccp4bb
last year. Here is the answer to that question.
Re: [ccp4bb]: Waters!
--------------------------------------------------------------------------------
To: r...@poori.biochem.uiowa.edu
Subject: Re: [ccp4bb]: Waters!
From: "Gerard \"DVD\" Kleywegt" <ger...@xray.bmc.uu.se>
Date: Wed, 7 Aug 2002 21:45:17 +0200 (CEST)
cc: Gerard Kleywegt <ger...@xray.bmc.uu.se>, CCP4 Bulletin Board
<ccp...@dl.ac.uk>
In-Reply-To:
<pine.lnx.4.33.0208071330010.2713-100...@poori.biochem.uiowa.edu>
Sender: owner-ccp...@dl.ac.uk
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> is there a program that will take a protein structure with waters and
> give a list of the waters that are buried/ or strip of the waters on the
> surface....
maybe unexpected, but MAMA actually does this. make a
quick and dirty mask around your molecule, expand a
couple of times, contract a couple of times (to fill
cavities etc) - then use the ATom_fit command; see
http://xray.bmc.uu.se/usf/mama_man.html#S22
--dvd
******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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At 09:01 AM 19/05/2003, Bartholomeus Kuettner wrote:
Dear PyMol community,
During analyzing the water structure of a protein I was wondering if PyMol
is capable to select buried water molecules. Since the surface waters occupy
clefts it would be nice to see if there is a regular distribution inside of
the protein as well.
So is it possible to make a selection of buried water molecules?
I imagine something in a way like 'water without distance to
surface-object'. But so far I didn't have yet such a deep dive into the
sophisticated selection capabilities of PyMol and would be lost here. The
problem I see arising would be that the surface object is present (as
residues) even in protein's interior and make a correct selection
impossible.
Greetings,
Bartholomeus
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