PyMOL Wiki - User contributions [en]

FindSurfaceResidues

2014-03-21T17:31:04Z

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

{{Infobox script-repo
|type = module
|filename = findSurfaceResidues.py
|author = [[User:inchoate|Jason Vertrees]]
|license = BSD-2-Clause
}}

<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>

= Overview =
This 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=False ]]]

The parameters are:

'''selection'''
:: The object or selection for which to find exposed residues;
:: DEFAULT = (all)
'''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
# now show the exposed
findSurfaceResidues doShow=True

# 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
</source>

= The Code =
<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):
"""
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')
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:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

Bondpack

2013-11-18T16:52:22Z

SebastianRaschka:

{{Infobox script-repo
|type = plugin
|filename = https://github.com/rasbt/BondPack
|author = Sebastian Raschka
|license = GNU GENERAL PUBLIC LICENSE
}}

== BondPack ==

A collection of PyMOL plugins to visualize atomic bonds. 

== Introduction ==
PyMOL is without any doubt a great tool to visualize protein and ligand molecules. 
However, drawing interactions between atoms can be often quite cumbersome when done manually. 
For the sake of convenience, I developed three plugins for PyMOL that will make our life as protein biologists a little bit easier. 
All three PyMOL plugins can be installed and used separately; they don't depend on each other, but rather complement each other. 
At the end of this article, you will find brief instructions on how to install plugins in PyMOL - a very quick and simple process. 

== HydroBond ==
HydroBond visualizes all potential polar contacts between protein and ligand molecules within a user-specified distance. 
The underlying function is based on the different atom types, such as hydrogen bond acceptor and donor atoms, 
and thus it is required to have hydrogen atoms present in the structure. 
If your structure file doesn't contain hydrogen atoms already, you can add them directly in PyMOL as shown in the image below. 
[[File:add_hydrogens.png]]
 HydroBond is related to PyMOLs "[A]->find->polar contacts" command, however, 
it doesn't consider geometry criteria and angle thresholds, but is rather based on atom types. 
When you select HydroBond from the "Plugin" menu, you will be prompted to enter the name of the protein object, 
the ligand object, and a distance cutoff as shown in the figure below. 
If HydroBond was able to detect hydrogen bond and acceptor atoms within the 
specified distance, potential interactions will be visualized as yellow dashed lines. 
[[File:hydrobond_action.png]]
 

== BondVis ==
The BondVis plugin lets you visualize interactions between any pair of atoms you specified. 
Often I find it helpful for my understanding (and for verification) to visualize the bonds between certain atoms 
that were assigned in docking or any other prediction software. 
Most software will provide you with information about the atoms that were "connected" to perform the analysis. 
If you run BondVis from the "Plugin" menu, it will ask you to select a "bond info file." 
[[File:bondinfo.png]]
 
This is just a simple text file that contains the atom numbers of connected atoms in pairs. 
Those can be separated by spaces, tabs, or commas. An example file with bond information could look like this: 
<code><pre>1174 1357
1175 1358
1176 1359
</pre></code>
 
When you selected a "bond info" file, BondVis will connect all atom pairs by yellow dashed lines 
and print out the connected atoms in the command field. 
[[File:bondvis.png]]
 

== BondLab ==
If you are not happy with the looks of the lines that were drawn to visualize connections between atoms, 
you will like to use BondLab. This plugin offers a simple interface that allows you to change the diameter, 
gap width, and color of the lines. 
[[File:bondlab.png]] 
The following video demonstrates the different features of BondLab: 
http://youtu.be/14UZctxtK3w
 
== Github ==
If you are interested, you can follow the BondPack Github repository 
https://github.com/rasbt/BondPack for updates

[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Plugins]]

User:SebastianRaschka

2013-11-18T16:40:03Z

SebastianRaschka: Created page with "Sebastian is a Ph.D. student at Michigan State University who works in a Computational Protein Structure Lab. He is developing a new drug screening approach based on a novel conc..."

Sebastian is a Ph.D. student at Michigan State University who works in a Computational Protein Structure Lab. He is developing a new drug screening approach based on a novel concept and likes to share the tools he is developing to aid his work.

If you like to contact me, my email address is se(dot)raschka(at)gmail(dot)com 
Or you can follow me on twitter @rasbt (https://twitter.com/rasbt)
I'd also be happy if you'd visit my website at http://sebastianraschka.com/

Main Page

2013-11-18T16:31:28Z

SebastianRaschka:

__NOTOC__
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|-
! New Plugin
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|-
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|-
! New Plugin
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|-
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|-
! New Script
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|-
! Tips & Tricks
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
|-
! New Script
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|-
! New Script
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|-
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|-
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|-
! New Script
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|-
! New Script
| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
|-
! New Script
| [[cyspka]] is an experimental surface cysteine pKa predictor.
|-
! New Plugin
| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
|-
! New Script
| [[spectrum_states]] colors states of multi-state object
|-
! New Script
| [[TMalign]] is a wrapper for the TMalign program
|-
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|-
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|-
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
|-
! Wiki Update
| Wiki has been updated. Please report any problems to the sysops.
|-
! New Scripts
| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
|-
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| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
|-
! New Script
| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
|-
! New Script
| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
|-
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Bondpack

2013-11-18T16:28:31Z

SebastianRaschka: first commit

File:Bondlab.png

2013-11-18T16:20:27Z

SebastianRaschka:

File:Bondvis.png

2013-11-18T16:20:10Z

SebastianRaschka:

File:Hydrobond action.png

2013-11-18T16:19:50Z

SebastianRaschka:

File:Bondinfo.png

2013-11-18T16:19:34Z

SebastianRaschka:

File:Add hydrogens.png

2013-11-18T16:19:07Z

SebastianRaschka: