PyMOL Wiki - User contributions [en]

User:B5foan

2009-09-15T13:39:50Z

B5foan:

Andreas Förster 
Postdoc at Imperial College London 
with PyMOL since at least 2001<br\><hr\>
http://www.msf.bio.ic.ac.uk/andreas.php

Protein contact potential

2009-06-24T13:41:16Z

B5foan:

<gallery heights="200px" widths="200px" caption="Comparing PyMOL-generated electrostatics and APBS' version." align="right">
Image:Prot_contact_pot.png|PyMOL Charge-smoothed potential (see below)
Image:Prot_contact_APBS.png|APBS-generated potential (see [[APBS]]).
</gallery>

[[Protein_contact_potential|Protein contact potential]] is an automated PyMOL representation where the false red/blue charge-smoothed surface is shown on the protein.

The rule of thumb with respect to PyMOL's internal "protein contact potential" is that if you care enough to be concerned with how it works, then you should instead be using a true Possion-Boltzman electrostatics solver such as [[APBS]].

Regardless, what PyMOL does to generate a qualitative electrostatic representation (via action '''popup->generate->vacuum electrostatics->...''') amounts to averaging charges over a small region of space using a
quasi-Coulombic-shaped convolution function. Nathan Baker has suggested that we simply refer to this approach as "charge smoothing".

PyMOL's use of the term "contact" relates to the fact that the potential shown by the default coloring approximates the potential that would be felt by a point-charge one solvent radius *above* the protein surface, if we ignore solvent screening and only consider nearby atoms. My personal opinion is that this sort of treatment makes a lot sense when viewing results from Poisson-Boltzmann calculations as well. (Select <tt>Color by potential on sol. acc. surf.</tt> in the visualization tab of the APBS plugin to get that effect.)

As an aside: It has never made any sense to me whatsoever that electrostatics visualization programs would show potentials located right on the molecular surface given that (1) we employ point charge models that have *only* been parameterized to approximate potential energies computed between partial charges located at atomic centers and that (2) the molecular surface is located in the region of space where artifacts & noise in a PB calculation would be greatest due to discrete discontinuities between the low-dielectric interior and the high-dielectric exterior (solvent region).

[[Category:Biochemical_Properties]]
[[Category:Electrostatics]]

APBS

2009-06-22T10:15:33Z

B5foan: /* Installing the Dependencies on OS X */

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

PyMol currently supports the '''APBS plugin''' written by Michael Lerner. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). See [http://apbs.wustl.edu/MediaWiki/index.php/APBS_electrostatics_in_PyMOL the APBS wiki] for more details, including instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
Note that the fink version of pymol '''already has''' the latest version of the APBS plugin. You are set to go!

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it.

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]

FindSurfaceResidues

2009-06-17T16:18:12Z

B5foan: /* Examples */

[[Image:FindExRes.png|thumb|right|400px|Result of $TUT/1hpv.pdb at 2.5 Ang cutoff.]]

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

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

= Usage =
<source lang="python">
findSurfaceResidues [objSel=(all)[, cutoff=2.5[, doShow=False[, verbose=False ]]]]
</source>
The parameters are:

'''objSel'''
:: 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
'''verbose'''
:: Level of verbosity.
:: 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
findSurface residues doShow=True

# watch how the visualization changes:
findSurfaceResidues doShow=True, cutoff=0.5
findSurfaceResidues doShow=True, cutoff=1.0
findSurfaceResidues doShow=True, cutoff=1.5
findSurfaceResidues doShow=True, cutoff=2.0
findSurfaceResidues doShow=True, cutoff=2.5
findSurfaceResidues doShow=True, 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()

selName = "exposed_" + str(random.randint(0,10000))
if verbose!=False:
print "Exposed residues are selected in: " + selName
cmd.select(selName, objSel + " in " + tmpObj )

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>

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]

User:B5foan

2007-10-24T15:59:41Z

B5foan:

Andreas Förster 
Postdoc at Imperial College London 
with PyMOL since at least 2001<br\><hr\>
https://www.biochem.utah.edu/~andreas

Ss

2007-10-24T14:53:46Z

B5foan:

A command to list a summary of the secondary structure for a selection. Use like "ss my_protein" where "my_protein" is the name of the chain or structure in view.

<source lang="python">
from pymol import cmd
from pymol import stored

def ss(selection):

class SSE(object):

def __init__(self, start, typ):
self.start, self.typ = start, typ
self.end = -1

def __repr__(self):
return "%s-%s %s" % (self.start, self.end, self.typ)

stored.pairs = []
cmd.iterate("%s and n. ca" % selection, "stored.pairs.append((resi, ss))")
num, currentType = stored.pairs[0]

sses = [SSE(num, currentType)]
currentSSE = sses[0]
for resi, ssType in stored.pairs:
if ssType == currentType:
currentSSE.end = resi
else:
sses.append(SSE(resi, ssType))
currentSSE = sses[-1]
currentType = ssType

for sse in sses:
print sse

cmd.extend("ss", ss)
</source>

User talk:B5foan

2005-12-09T09:15:12Z

B5foan:

regular user

User:B5foan

2005-12-09T09:13:52Z

B5foan:

Andreas Förster 
Postdoc at Institut de Biologie Structurale 
with PyMOL since at least 2001<br\><hr\>
http://www.biochem.utah.edu/~andreas/index_e.html

User:B5foan

2005-12-09T09:13:24Z

B5foan:

Andreas Förster 
Postdoc at Institut de Biologie Structurale 
with PyMOL since at least 2001<br\><hr\>
http://biochem.utah.edu/~andreas/index_e.html

User:B5foan

2005-12-09T09:12:12Z

B5foan:

Andreas Förster 
Postdoc at Institut de Biologie Structurale 
with PyMOL since at least 2001<br\><hr\>
<nowiki><a href="http://biochem.utah.edu/~andreas/index_e.html" title="my homepage">Check me out</a></nowiki>

User:B5foan

2005-12-09T09:10:22Z

B5foan:

Andreas Förster 
Postdoc at Institut de Biologie Structurale 
with PyMOL since at least 2001<br\><hr\>
<a href="http://biochem.utah.edu/~andreas/index_e.html" title="my homepage">Check me out</a>

User:B5foan

2005-12-09T09:08:12Z

B5foan: DocAndreas

Andreas Förster
Postdoc at Institut de Biologie Structurale
with pymol since at least 2001

Main Page

2005-11-28T08:39:01Z

B5foan:

== PyMol Wiki Home ==
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.

We provide
* updates on [http://pymol.sf.net PyMol]
* a stable user-oriented documentation base
* a thorough treatment of the PyMol program
* feature-rich scripts for general PyMol use

==News==
* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.
* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].
* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]
* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.
* Added [[Kabsch]] script for optimal alignment of two sets of vectors.
* Some details have been released about [[0.99beta11]]'s release and new features.
* A new map function is in the beta build, [[Map_Trim]].
* Details on how to build [[Peptide_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| nucleic acid sequences]] by hand.
* New [[Transform_odb]] script to transform coordinates with .odb file from O or LSQMAN

See our [[Older_News]].

== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]