FindSurfaceResidues - Revision history

Cchem: 1 revision

2019-04-01T03:11:56Z

1 revision

Speleo3: removed outdated code

2019-03-29T07:42:06Z

removed outdated code

Show changes

Bell: 1 revision

2014-06-09T14:21:52Z

1 revision

Andwar: changed (commented) a line in the surfaceatoms function (section: if show!=False); altering vdw affects repeated runs and was replaced by adjusting sphere_scale instead

2014-06-01T22:56:28Z

changed (commented) a line in the surfaceatoms function (section: if show!=False); altering vdw affects repeated runs and was replaced by adjusting sphere_scale instead

Pyadmin: 10 revisions

2014-03-28T02:00:43Z

10 revisions

SebastianRaschka: fixed a typo: should be "findSurfaceResidues doShow=True" instead of "findSurface residues doShow=True

2014-03-21T17:31:04Z

fixed a typo: should be "findSurfaceResidues doShow=True" instead of "findSurface residues doShow=True

Speleo3: script-repo

2013-07-14T18:56:34Z

script-repo

Tlinnet: /* The Code */

2011-08-24T13:59:25Z

The Code

Hongbo zhu: /* The Code */

2011-05-14T21:11:05Z

The Code

Hongbo zhu: /* Overview */

2011-05-14T21:04:01Z

Overview

@@ Line 175: / Line 175: @@
 		cmd.util.cbaw(selNameRes)
 		cmd.disable(selNameRes)
-		cmd.alter('%s'%(selName),'vdw=0.5')
+		#cmd.alter('%s'%(selName),'vdw=0.5') # affects repeated runs
 		cmd.show("spheres", "%s"%selName)
 		cmd.util.cbao(selName)

@@ Line 1: / Line 1: @@
 <gallery>
 Image:FindExRes.png|thumb|right|300px|Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.
@@ Line 12: / Line 19: @@
 = Usage =
-<source lang="python">
-findSurfaceResidues [objSel=(all)[, cutoff=2.5[, doShow=False[, verbose=False ]]]]
+ findSurfaceResidues [ selection=all [, cutoff=2.5 [, doShow=False ]]]
-</source>
 The parameters are:
-'''objSel'''
+'''selection'''
 :: The object or selection for which to find exposed residues;
 :: DEFAULT = (all)
@@ Line 25: / Line 32: @@
 '''doShow'''
 :: Change the visualization to highlight the exposed residues vs interior
 :: DEFAULT = False/Blank
@@ Line 39: / Line 43: @@
 # watch how the visualization changes:
-findSurfaceResidues doShow=True, cutoff=0.5
+findSurfaceResidues doShow=1, cutoff=0.5
-findSurfaceResidues doShow=True, cutoff=1.0
+findSurfaceResidues doShow=1, cutoff=1.0
-findSurfaceResidues doShow=True, cutoff=1.5
+findSurfaceResidues doShow=1, cutoff=1.5
-findSurfaceResidues doShow=True, cutoff=2.0
+findSurfaceResidues doShow=1, cutoff=2.0
-findSurfaceResidues doShow=True, cutoff=2.5
+findSurfaceResidues doShow=1, cutoff=2.5
-findSurfaceResidues doShow=True, cutoff=3.0
+findSurfaceResidues doShow=1, cutoff=3.0
 </source>

← Older revision		Revision as of 13:59, 24 August 2011
Line 114:		Line 114:

	cmd.extend("findSurfaceResidues", findSurfaceResidues)		cmd.extend("findSurfaceResidues", findSurfaceResidues)
		+	</source>
		+
		+	= Another version =
		+	<gallery heights="240px" widths="340px">
		+	Image:Surfaceatoms.png\|Another version, to show the same thing. The part of the protein which is not surface exposed is in cartoon. The white is the surface "byres" exposed residues shown in sticks. The orange is the atoms which is exposed.
		+	</gallery>
		+
		+	<source lang="python">
		+	from pymol import cmd, stored
		+
		+	def surfaceatoms(molecule="NIL",show=True, verbose=True, cutoff=2.5):
		+	"""
		+	surfaceatoms
		+	finds those residues on the surface of a protein
		+	that have at least 'cutoff' exposed A**2 surface area.
		+	PARAMS
		+	molecule (string)
		+	the object or selection in which to find
		+	exposed residues
		+	DEFAULT: (last molecule in pymol)
		+	cutoff (float)
		+	your cutoff of what is exposed or not.
		+	DEFAULT: 2.5 Ang**2
		+	RETURNS
		+	(list: (chain, resv ) )
		+	A Python list of residue numbers corresponding
		+	to those residues w/more exposure than the cutoff.
		+	"""
		+	if molecule=="NIL":
		+	assert len(cmd.get_names())!=0, "Did you forget to load a molecule? There are no objects in pymol."
		+	molecule=cmd.get_names()[-1]
		+	tmpObj="__tmp"
		+	cmd.create(tmpObj, "(%s and polymer) and not resn HOH"%molecule)
		+	if verbose!=False:
		+	print "WARNING: I'm setting dot_solvent. You may not care for this."
		+	cmd.set("dot_solvent")
		+	cmd.get_area(selection=tmpObj, load_b=1)
		+	# threshold on what one considers an "exposed" atom (in A**2):
		+	cmd.remove( tmpObj + " and b < " + str(cutoff) )
		+	stored.tmp_dict = {}
		+	cmd.iterate(tmpObj, "stored.tmp_dict[(chain,resv)]=1")
		+	exposed = stored.tmp_dict.keys()
		+	exposed.sort()
		+
		+	selName = "%s_atoms"%molecule
		+	cmd.select(selName, molecule + " in " + tmpObj )
		+	if verbose!=False:
		+	print "Exposed residues are selected in: " + selName
		+	selNameRes = "%s_resi"%molecule
		+	cmd.select(selNameRes, "byres " + selName )
		+
		+	if show!=False:
		+	cmd.hide("everything", molecule)
		+	cmd.show("cartoon", "%s and not %s and not resn HOH"%(molecule,selNameRes))
		+	cmd.show("sticks", "%s"%selNameRes)
		+	cmd.util.cbaw(selNameRes)
		+	cmd.disable(selNameRes)
		+	cmd.alter('%s'%(selName),'vdw=0.5')
		+	cmd.show("spheres", "%s"%selName)
		+	cmd.util.cbao(selName)
		+	cmd.disable(selName)
		+
		+	cmd.delete(tmpObj)
		+	print(exposed)
		+	return(exposed)
		+	cmd.extend("surfaceatoms", surfaceatoms)
	</source>		</source>

@@ Line 94: / Line 94: @@
 	exposed.sort()
-	selName = "exposed_" + str(random.randint(0,10000))
+        randstr = str(random.randint(0,10000))
 	if verbose!=False:
 		print "Exposed residues are selected in: " + selName
 	cmd.select(selName, objSel + " in " + tmpObj )
 	if doShow!=False:

@@ Line 6: / Line 6: @@
 = Overview =
-This script will select (and color if requested) surface residues on an object or selection.  See the options below.
+This script will select (and color if requested) surface residues and atoms on an object or selection.  See the options below.
 = Usage =

← Older revision	Revision as of 03:11, 1 April 2019
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← Older revision	Revision as of 14:21, 9 June 2014
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