[PyMOL] Upgraded computer, PyMol now unusable :^(

2009-10-23 Thread John Ladasky
Hi folks,   I was using PyMol with no problems about a year ago.  I believe that my PyMol version was in the 0.9x series.  I was using Ubuntu Linux 6.06 on a Pentium IV machine.   Since then I have upgraded to a new multi-core motherboard, and Ubuntu Linux 8.04.  The Linux repository has a

[PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

2009-10-23 Thread John Ladasky
Hello again,   With some hints from Ubuntu Forums, I tracked down and corrected my problem.  Hopefully this will be of help to someone else.   The fancy new desktop rendering schemes which are part of Ubuntu v.8, but which were not part of Ubuntu v.6, use 3D graphics to grow, shrink, and move

Re: [PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

2009-10-23 Thread Maia Cherney
Hi John, I have a similar problem with my ubuntu 8.10. When I use a command window, I get the error message: Traceback (most recent call last): File /var/lib/python-support/python2.5/pymol//__init__.py, line 167, in module import pymol File

Re: [PyMOL] Export trajectory

2009-10-23 Thread Sean Law
Andrea, I use MD quite a lot myself and we have some in-house tools that perform this function (converting a set of PDB files into a trajectory). However, I took it upon myself as a challenge to see if I could implement this into PyMOL as a Python script. Thus, last night I worked

[PyMOL] Replace Coordinates in State

2009-10-23 Thread Sean Law
Hi All, I was wondering if there was a faster way to replace all coordinates. I've used commands such as iterate_state and alter_state before but they are far too slow since they have to iterate over each atom. Instead, I want to replace one set of coordinates that correspond to a specific