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Find buried waters - Revision history
2026-05-25T01:35:42Z
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2014-03-28T02:16:24Z
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Pyadmin
https://wiki.pymol.org/index.php?title=Find_buried_waters&diff=7958&oldid=prev
Speleo3: make it work with plugin manager, add state and quiet arguments, fix cutoff argument, add docstring
2012-06-11T19:59:50Z
<p>make it work with plugin manager, add state and quiet arguments, fix cutoff argument, add docstring</p>
<p><b>New page</b></p><div>This script finds and turns a selection of waters determined to be buried (no solvent accessibility) in the original selection. If you prefer to define your own cutoff of "accessible" use the 2nd parameter.<br />
<br />
== Usage ==<br />
<br />
find_buried_waters [ sele [, cutoff [, state ]]]<br />
<br />
== Script ==<br />
<br />
<source lang="python"><br />
from pymol import cmd<br />
<br />
def find_buried_waters(sele='all', cutoff=-1, state=1, quiet=1, _self=cmd):<br />
'''<br />
DESCRIPTION<br />
<br />
Finds and turns a selection of waters determined to be buried (no solvent<br />
accessibility) in the original selection.<br />
<br />
ARGUMENTS<br />
<br />
sele = string: atom selection {default: all}<br />
<br />
cutoff = float: threshold on what one considers an "exposed"<br />
atom (in A**2) {default: surface_residue_cutoff}<br />
<br />
state = int: object state {default: 1}<br />
'''<br />
cutoff, state, quiet = float(cutoff), int(state), int(quiet)<br />
<br />
tmpObj=_self.get_unused_name("__tmp")<br />
_self.create(tmpObj, sele, state, 1, zoom=0)<br />
<br />
_self.set("dot_solvent", 1, tmpObj);<br />
_self.get_area(tmpObj, state=1, load_b=1)<br />
<br />
if cutoff < 0:<br />
cutoff = _self.get("surface_residue_cutoff")<br />
_self.remove(tmpObj + " and not solvent")<br />
_self.remove(tmpObj + " and b > %s" % cutoff)<br />
<br />
exposed = set()<br />
_self.iterate(tmpObj, "exposed.add((chain,resv))", space=locals())<br />
<br />
selName = _self.get_unused_name("buried")<br />
_self.select(selName, "(%s) in %s" % (sele, tmpObj))<br />
<br />
# clean up<br />
_self.delete(tmpObj)<br />
<br />
if not quiet:<br />
print ' Found %d buried water atoms' % (len(exposed))<br />
<br />
return sorted(exposed)<br />
<br />
cmd.extend('find_buried_waters', find_buried_waters)<br />
</source><br />
<br />
== See Also ==<br />
<br />
* [[Get_Area|get_area]]<br />
* [[FindSurfaceResidues]]<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]</div>
Speleo3