PyMOL Wiki - User contributions [en]

Linux Install

2007-03-12T10:17:40Z

Pierre: /* libnvidia-tls.so.1: cannot handle TLS data */

Installing PyMol is quite straightforward.

=PyMol=
Installing PyMol is very simple, even from source. On Linux, you need the following requirements:
* [http://www.python.org/ Python] (with distutils)
* [http://pmw.sf.net Pmw] (Python Megawidgets)
* OpenGL driver (I use [http://www.nvidia.com/object/unix.html NVidia])

== Generic Linux ==

=== 0.99rc1 note! ===
For those keeping current via CVS, building from source, or installing precompiled unix binaries, here is a quick "heads up!" intended to save you some minor grief: For the last six years, the PyMOL launch script has been called '''pymol.com''' instead of simply "pymol". I can't remember why I did things that way, but PyMOL's ".com" convention is different from the most everything else and for no good reason. The launch script should just be the name of the program.

Therefore, as of 0.99rc1, the launch script will simply be "pymol". No big deal right? Well, not so fast: symbolic links, shell aliases, external scripts, package builders, and end-user habits may all need to be adjusted after installing this next version. That is why I haven't changed this before now -- but we should clean this up before 1.0. So, remember: if you update to PyMOL 0.99rc1 (when it's released) and suddenly can't launch PyMOL, that is likely what is going on. Either reset your pointers to '''./pymol''', or symlink '''./pymol''' to '''./pymol.com''' to preserve the status quo.

=== From Source ===
* untar the compressed package;
* cd into the newly untarred directory (should be '''pymol''' or '''pymol-version''').
* execute <source lang="python">python setup.py install # you may need to be root</source>
* execute <source lang="python">python setup2.py install # you may need to be root</source>
* execute <source lang="python">cp ./pymol.com SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
or for the latest version,
* execute <source lang="python">cp ./pymol SOME_PATH # where SOME_PATH is some directory in your $PATH</source>
The executable name is "pymol.com".

=== From Package ===
Download the appropriate RPM and use 'rpm' to install it. Typically,
rpm -Uvh rpmFileName.rpm

===Compiling By Hand===
Due to the large variance of Linux systems, some systems may work fine with PyMol, and some may have related install issues. To overcome this, you can download the '''ext''' package and the PyMol source and compile/install by hand.

Once downloaded, see the file '''pymol/INSTALL''' and '''pymol/INSTALL.generic'''.

Here's the basic steps to install by source:
# get the source [http://delsci.com/rel/0_98/#OtherUnix PyMol Source]
# extract both packages, rename ext-VERSION.tgz to ext and move it into the pymol directory
# cd pymol
# cd ext
# vi build.com # edit the build file
# cd ..
# cp setup/Rules.make . # or correct Rules.make file for your machine
# vi Rules.make # make appropriate changes
# vi setup.py # make appropriate changes
# make

Warnings:
* if you're using a 64-bit machine, lib becomes lib64 for almost everything
* ensure you have the correct Python path and version (is it 2.3? 2.4?)
* make sure you make the changes in '''Rules.make''', '''setup.py''', and '''Makefile''', for your platform.

Copy the appropriate setup/Rules.XXX file to the base PyMol dir. You'll have to edit the file for your system. Then run 'make'.

== Fedora Core Linux (x86) ==
PyMOL RPMs are available for Fedora Core 1 & 2, provided by Morten Kjeldgaard. These can be manually downloaded by browsing from: [http://apt.bioxray.dk/]

Alternatively, PyMOL can be installed using [http://linux.duke.edu/projects/yum/ Yum] (an automated package installer and updater, installed by default in Fedora). This can be done by adding the following lines to your /etc/yum.conf file:

[xray]
name=MOKs RPM Repository fedora $releasever - $basearch - xray
baseurl=http://apt.bioxray.dk/fedora/fc$releasever/$basearch/xray

you may also need to add the pgp key for the repository before yum will get packages from it by either saying:

rpm --import http://www.bioxray.dk/~mok/404825e7.asc

or with older versions of rpm:

wget http://www.bioxray.dk/~mok/404825e7.asc
rpm --import 404825e7.asc

And then issuing the following command as root:

yum install pymol

== Gentoo Linux (x86) ==
as root:
emerge pymol
be sure to have the proper OpenGL configuration. For example:
opengl-update ati
opengl-update nvidia
list of available versions of [http://packages.gentoo.org/packages/?category=sci-chemistry;name=pymol pymol for gentoo]

== SuSe ==
=== 32-bit (x86) ===
See [[#Generic Linux]] above.

=== 64-bit (x86_64) ===
See [[#Generic Linux]] above. Some details for problem solving are here. 64-bit Python install is quite easy. Make sure your nvidia driver is installed (or ATI, but I have no experience there).

To install PyMol
*Ensure your system has it's distutils in place and ready to use. Try the following check:
<source lang="python">
from distutils import *
</source>
*Download the [http://pymol.org/ source]
*Download [http://www.sf.net/projects/pmw Pmw] from [http://www.sf.net/ SourceForge].
** To install Pmw, just decompress it and then move the base director "Pwm" to /usr/lib64/python2.3/site-packages/. You can test that it's there by testing the import, see below:
<source lang="python">
import * from Pmw
</source>
If errors erupt, investigate.
* decompress the source and cd into the PyMol directory that was just decompressed.
* If upgrading see [[:Category: Upgrading PyMol|below]].
* Now enter the following...
<code>
python setup.py build<br>
sudo python setup.py install<br>
sudo python setup2.py
</code>
* The sudo commands will need a root password or someone with sudo capabilities.

I also copy the 'pymol.com' file to /usr/local/bin or /usr/bin -- somewhere in my path:
<source lang="python">
sudo cp ./pymol.com /usr/local/bin
</source>
Please note that newer versions of PyMol create the '''pymol''' executable, not '''pymol.com'''. So, for later versions (~0.99+) use
<source lang="python">
sudo cp ./pymol /usr/local/bin
</source>

You should now have a working PyMol install.

'''pymol.com''' should now run your new PyMol install.

==Ubuntu Linux (x86 32,64; mac ppc)==

http://xanana.ucsc.edu/~wgscott/xtal/ubuntu-small.png

The [http://www.ubuntu.com/ Ubuntu] [http://packages.ubuntu.com/breezy/science/pymol pymol package] can be installed with minimal effort using the GUI package manager [http://en.wikipedia.org/wiki/Synaptic_Package_Manager synaptic], or on the command line, using the command

sudo apt-get install pymol

once the [http://ubuntuguide.org/#extrarepositories universe repository] has been activated.

[http://en.wikipedia.org/wiki/Ubuntu_Linux Ubuntu] is a completely free and well-maintained Debian GNU/Linux distribution. Further details on using [http://xanana.ucsc.edu/linux/debian_linux.html Ubuntu for crystallography] and related applications are available are linked. PyMol also compiles from source on Ubuntu following the [[#Generic Linux]] instructions given above.

=Preparing your System=
See [[Linux_XFree86_Configuration]].

==Graphics==
===XFree86 Config===
Check out [[XFree86_Configuration|Configuring XFree86]] if you need information on editing the XFree86 configuration file.

[[Category:Installation|Linux Installation]]

===Xorg===
Adding a
Stereo 3
option in /etc/X11/xorg.conf suffices to run pymol in stereo mode on a 64bit system with the Nvidia Quadro FX1400 under Red Hat Enterprise 4 (RHEL4). Adding the following modeline (determined via /usr/bin/gtf):

ModeLine "1280x1024_118.00" 229.7 1280 1384 1528 1776 1024 1025 1028 1096 -hsync +vsync

appears to slightly improve the stereo quality, in particular when one
displays labels and/or dashes/dots.

For those having possible driver issues, this link might help
[http://www.nvnews.net/vbulletin/showthread.php?t=69136 NVNews]

=Problems=

==Input==
If you notice that the keyboard input is ignored into the Pmw widgets, you may have an X-based input method editor installed and running. Such examples could be SCIM, KINPUT/2 or the like. Try turning off the IME and restarting PyMol to get the widgets to recognize your input.

==libnvidia-tls.so.1: cannot handle TLS data==

If you get an error, upon invoking pymol, of the form

<pre>
Traceback (most recent call last):
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 109, in ?
import pymol
File "/usr/lib/python2.4/site-packages/pymol/__init__.py", line 353, in ?
import _cmd
ImportError: libnvidia-tls.so.1: cannot handle TLS data
</pre>

then try changing the permissons on libnvidia-tls.so.1. i.e,

<pre> sudo chmod 777 /usr/lib/libnvidia-tls.so.1 </pre>

Category:Uncategorized

2007-01-16T08:56:53Z

Pierre: /* Van der Waals radii */

==Alter key bindings==
It's not GUI, but you could simply bind a function key such as F1 to a command:
<source lang="python">
cmd.set_key('F1',lambda :cmd.show('sticks'))
</source>

==Coloring Surface with Electrostatic Potential==
You have to load the potential data by Delphi or some other program like AMBER version 9:
<source lang="python">
load sample.pdb, molecule
load sample.delphi, potential
show surface, molecule
ramp_new level, potential, [-7,0,7]
set surface_color, level, molecule
</source>

==Van der Waals radii==
van der Waals Radii are hard coded in Pymol.
They may be obtained for given atoms from:
<source lang="python">
iterate (name C), print vdw
</source>
Default values are:
*C : 1.70
*O : 1.52
*N : 1.55
*H : 1.20
*P : 1.80

and may be changed with the command [[alter]]

Category:Uncategorized

2007-01-16T08:55:55Z

Pierre:

Iterate

2007-01-16T08:49:34Z

Pierre: /* DESCRIPTION */

===DESCRIPTION===
'''iterate''' iterates over an expression with a separate name space for each atom. However, unlike the "alter" command, atomic properties can not be altered. Thus, '''iterate''' is more efficient than '''alter'''.

It can be used to perform operations and aggregations using atomic selections, and store the results in any global object, such as the predefined '''stored''' object.

The local namespace for "iterate" contains the following names:
*name
*resn
*resi
*chain
*alt
*elem
*q
*b
*segi
*type (ATOM,HETATM)
*formal_charge
*partial_charge
*numeric_type
*text_type
*ID
*vdw

All strings in the expression must be explicitly quoted. This operation typically takes a second per thousand atoms.

===USAGE===
iterate (selection),expression

===EXAMPLES===
*The following example calculates the net charge on an object.
<source lang="python">
stored.net_charge = 0
iterate (all),stored.net_charge = stored.net_charge + partial_charge
</source>

*The following example fills an array, '''stored.names''' with the names of all the residues.
<source lang="python">
stored.names = []
iterate (all),stored.names.append(name)
</source>

*The following prints the b-factors for all atoms around residue #1.
<source lang="python">
iterate resi 1, print round(b,2)
</source>

===SEE ALSO===
[[Cmd iterate_state]], [[Cmd alter]], [[Cmd alter_state]]

[[Category:Commands|iterate]]

Alter

2007-01-16T08:45:19Z

Pierre: /* EXAMPLES */

===DESCRIPTION===
'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===

* Change chain label and residue index
<source lang="python">
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
</source>

* Change van der Waals radius of a given atom
<source lang="python">
alter (name P), vdw=1.90
</source>
Not that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
<source lang="python">
rebuild
</source>

===SEE ALSO===
[[Cmd alter_state]], [[Cmd iterate]], [[Cmd iterate_state]], [[Cmd sort ]]

[[Category:Commands|alter]]

Alter

2007-01-16T08:42:12Z

Pierre: /* EXAMPLES */

===DESCRIPTION===
'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===

* Change chain label and residue index
<source lang="python">
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
</source>

* Change van der Waals radius of a given atom
<source lang="python">
alter (name P), vdw=1.90
</source>

===SEE ALSO===
[[Cmd alter_state]], [[Cmd iterate]], [[Cmd iterate_state]], [[Cmd sort ]]

[[Category:Commands|alter]]

Alter

2007-01-16T08:38:21Z

Pierre: /* DESCRIPTION */

===DESCRIPTION===
'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort

===SEE ALSO===
[[Cmd alter_state]], [[Cmd iterate]], [[Cmd iterate_state]], [[Cmd sort ]]

[[Category:Commands|alter]]