FindSurfaceResidues: Difference between revisions

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<gallery>
The [[findSurfaceResidues]] script will select (and color if requested) surface residues and atoms on an object or selection. See the options below.
Image:FindExRes.png|thumb|right|300px|Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.
Image:Surface_residues_ex.png|300px|Example coloring of surface residues
</gallery>


Each time, the script will create two new selections called, '''exposed_res_XYZ''' and '''exposed_atm_XYZ''' where ''XYZ'' is some random number.  This is done so that no other selections/objects are overwritten.


= Overview =
= Usage =
This script will select (and color if requested) surface residues and atoms on an object or selection.  See the options below.


findSurfaceResidues [ selection=all [, cutoff=2.5 [, doShow=0 ]]]


Each time, the script will create two new selections called, 'exposed_res_XYZ' and 'exposed_atm_XYZ' where XYZ is some random number.  This is done so that no other selections/objects are overwritten.
= Arguments =


= Usage =
* '''selection''' = str: The object or selection for which to find exposed residues {default: all}
* '''cutoff''' = float: The cutoff in square Angstroms that defines exposed or not. Those atoms with > cutoff Ang^2 exposed will be considered ''exposed'' {default: 2.5 Ang^2}
* '''doShow''' = 0/1: Change the visualization to highlight the exposed residues vs interior {default: 0}


findSurfaceResidues [ selection=all [, cutoff=2.5 [, doShow=False ]]]
= Examples =


The parameters are:
<gallery>
Image:FindExRes.png|thumb|right|300px|Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.
Image:Surface_residues_ex.png|300px|Example coloring of surface residues
</gallery>


'''selection'''
<source lang="python">
:: The object or selection for which to find exposed residues;
run findSurfaceResidues.py
:: DEFAULT = (all)
fetch 1hpv, async=0
'''cutoff'''
:: The cutoff in square Angstroms that defines exposed or not.  Those residues with > cutoff Ang^2 exposed will be considered ''exposed'';
:: DEFAULT =  2.5 Ang^2
'''doShow'''
:: Change the visualization to highlight the exposed residues vs interior
:: DEFAULT = False/Blank


== Examples ==
<source lang="python">
# make sure you download and run the code below, before trying these examples.
load $TUT/1hpv.pdb
findSurfaceResidues
findSurfaceResidues
# now show the exposed
# now show the exposed
findSurfaceResidues doShow=True
findSurfaceResidues doShow=1


# watch how the visualization changes:
# watch how the visualization changes:
Line 51: Line 45:
</source>
</source>


= The Code =
= See Also =
<source lang="python">
# -*- coding: utf-8 -*-
import pymol
from pymol import cmd
import random


def findSurfaceResidues(objSel="(all)", cutoff=2.5, doShow=False, verbose=False):
* [[get_sasa_relative]]
"""
* [[Get_Area|get_area]]
findSurfaceResidues
finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
 
PARAMS
objSel (string)
the object or selection in which to find
exposed residues
DEFAULT: (all)
 
cutoff (float)
your cutoff of what is exposed or not.
DEFAULT: 2.5 Ang**2
 
asSel (boolean)
make a selection out of the residues found
 
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
 
"""
tmpObj="__tmp"
cmd.create( tmpObj, objSel + " and polymer");
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()
 
        randstr = str(random.randint(0,10000))
selName = "exposed_atm_" + randstr
if verbose!=False:
print "Exposed residues are selected in: " + selName
cmd.select(selName, objSel + " in " + tmpObj )
        selNameRes = "exposed_res_" + randstr
        cmd.select(selNameRes, "byres " + selName )
 
 
if doShow!=False:
cmd.show_as("spheres", objSel + " and poly")
cmd.color("white", objSel)
cmd.color("red", selName)
 
cmd.delete(tmpObj)
 
return exposed
 
 
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') # affects repeated runs
                cmd.set('sphere_scale','0.3','%s'%(selName)) # does not affect repeated runs
cmd.show("spheres", "%s"%selName)
cmd.util.cbao(selName)
cmd.disable(selName)
 
cmd.delete(tmpObj)
print(exposed)
return(exposed)
cmd.extend("surfaceatoms", surfaceatoms)
</source>


[[Category:Script_Library]]
[[Category:Script_Library]]
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[[Category:Biochemical_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Structural_Biology_Scripts]]
__NOTOC__

Latest revision as of 02:42, 29 March 2019

Type Python Module
Download findSurfaceResidues.py
Author(s) Jason Vertrees
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

The findSurfaceResidues script will select (and color if requested) surface residues and atoms on an object or selection. See the options below.

Each time, the script will create two new selections called, exposed_res_XYZ and exposed_atm_XYZ where XYZ is some random number. This is done so that no other selections/objects are overwritten.

Usage

findSurfaceResidues [ selection=all [, cutoff=2.5 [, doShow=0 ]]]

Arguments

  • selection = str: The object or selection for which to find exposed residues {default: all}
  • cutoff = float: The cutoff in square Angstroms that defines exposed or not. Those atoms with > cutoff Ang^2 exposed will be considered exposed {default: 2.5 Ang^2}
  • doShow = 0/1: Change the visualization to highlight the exposed residues vs interior {default: 0}

Examples

  • Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.

    Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.

  • Example coloring of surface residues

    Example coloring of surface residues 

run findSurfaceResidues.py
fetch 1hpv, async=0

findSurfaceResidues

# now show the exposed
findSurfaceResidues doShow=1

# watch how the visualization changes:
findSurfaceResidues doShow=1, cutoff=0.5
findSurfaceResidues doShow=1, cutoff=1.0
findSurfaceResidues doShow=1, cutoff=1.5
findSurfaceResidues doShow=1, cutoff=2.0
findSurfaceResidues doShow=1, cutoff=2.5
findSurfaceResidues doShow=1, cutoff=3.0

See Also

Retrieved from "https://pymolwiki.org/index.php?title=FindSurfaceResidues&oldid=12902"