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:war...@delanoscientific.com
Warren L. DeLano
Principal
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Bartholomeus Kuettner
Sent: Sunday, May 18, 2003 3:02 PM
To: pymol-users@lists.sourceforge.net
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
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