From: Bartholomeus K. <bku...@ep...> - 2003-05-18 23:04:40
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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 |
From: Warren L. D. <wa...@de...> - 2003-05-20 20:02:15
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Bartholemeus, No, there isn't any way to do this directly with the selection language. The closest you can get is to simply select the waters in proximity to protein atoms. select close_waters, hoh/ within 3.1 of not hoh/ You could then use some external tool to calculate the SASA of these waters to determine whether or not they are buried. However, try the following script -- it may get close to what you want. Note however that the van der Waals "overlap" command isn't yet validated or documented. # begin "buried.pml" load $PYMOL_PATH/test/dat/1tii.pdb hide show sph,hoh/ show surface set surface_color,white /wats = map(lambda x:"%s`%d"%x,cmd.index("hoh/")) /over = map(lambda x: \ (cmd.overlap(x,"not hoh/",adjust=5.0),x), wats) # least buried color green,hoh/ /for a in filter(lambda x:x[0]>25, over): \ cmd.color("cyan",a[1]) /for a in filter(lambda x:x[0]>50, over): \ cmd.color("blue",a[1]) /for a in filter(lambda x:x[0]>75, over): \ cmd.color("yellow",a[1]) # most buried /for a in filter(lambda x:x[0]>100, over): \ cmd.color("red",a[1]) # now show interior... clip slab,10 # end of script Cheers, Warren -- mailto:wa...@de... Warren L. DeLano Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Bartholomeus Kuettner Sent: Sunday, May 18, 2003 3:02 PM To: pym...@li... Subject: [PyMOL] select buried water molecules 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 ------------------------------------------------------- This SF.net email is sponsored by: If flattening out C++ or Java code to make your application fit in a relational database is painful, don't do it! Check out ObjectStore. Now part of Progress Software. http://www.objectstore.net/sourceforge _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Anthony D. <A....@us...> - 2003-05-21 00:48:50
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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 > > >------------------------------------------------------- >This SF.net email is sponsored by: If flattening out C++ or Java >code to make your application fit in a relational database is painful, >don't do it! Check out ObjectStore. Now part of Progress Software. >http://www.objectstore.net/sourceforge >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- |