Re: [PyMOL] select buried water molecules

[Anthony D. <A....@us...>]

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: ra...@po...
>Subject: Re: [ccp4bb]: Waters!
>From: "Gerard \"DVD\" Kleywegt" <ge...@xr...>
>Date: Wed, 7 Aug 2002 21:45:17 +0200 (CEST)
>cc: Gerard Kleywegt <ge...@xr...>, CCP4 Bulletin Board 
><CC...@dl...>
>In-Reply-To: 
><Pin...@po...>
>Sender: own...@dl...
>
>--------------------------------------------------------------------------------
>
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> > 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:ge...@xr...
>******************************************************************
>    The opinions in this message are fictional.  Any similarity
>    to actual opinions, living or dead, is purely coincidental.
>******************************************************************





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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----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-7817   Fax. 61-2-9351-4726
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