PyMOL
by Delano Scientific
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
Please cite PyMOL in publications and presentations:
Warren L. DeLano "The PyMOL Molecular Graphics System."
DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org
Running PyMOL
chmsgi and any SGI machine that is running IRIX 6.5 or later and has chmsgi:/chem mounted you will need to add the following alias to your .tcshrc file:
alias pymol /chem/pymol/pymol_0.95/pymol.com
k2 - you will need to add the following alias to your .tcshrc file:
alias pymol /usr/local/lms/pymol/pymol_0.95/pymol.com
PyMOL is also available for MacOS X/X11, PC, Sun, and Linux. Please visit the
PyMOL Homepage to download the executables for these other platforms.
Trouble-Shooting
error:
pymol: Command not found.
The alias that you created in your .tcshrc is either incorrect or has not been activated yet. Check the line in your .tcshrc file and make sure it matches the commands given above. To activate the
modified .tcshrc you may log out and log back in or simply type:
The source command will activate any changes made to your .tcshrc file.
If you are running on a remote machine and you receive the error:
Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0
(where labmol4.chem.tamu.edu will be replaced by the local machine name)
You need to use X11 forwarding to access the remote machine (ssh -X
username@
remote_machine_name or you may also need to use the -Y flag
ssh -X -Y
username@
remote_machine_name )
