RE: [PyMOL] select buried water molecules

[Warren L. D. <wa...@de...>]

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


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