Re: [PyMOL] DNA ligand presentation in PyMOL

Hi Amna, DNA molecule has internal HBONDS too.. how can i see the hbonds made between just ligand and DNA, ??? If there is nothing else than DNA and ligand, this should probably work (otherwise, be more precise with the selections...): PyMOL distance hbonds, (polymer), (organic), mode=2 how

Re: [PyMOL] stick/ribbon rendering not working

Hi Abhinav, Does this setting help: set cylinder_shader_ff_workaround, 1 If not, can you please send me a screenshot showing the problem? Cheers, -- Jason On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote: Hi, I recently upgraded my desktop to Ubuntu 12.10.

[PyMOL] get_dihedral for multiple files(states of a movie)

Hello all, I have generated a movie of 300 snapshots (MD simulation trajectory). How can i calculate dihedral angles for same four atoms across the trajectory (or a movie)?? I mean get_dihedral 58/n,58/c,58/ca,58/cb values 300 times for each snapshot. Regards Tasneem

Re: [PyMOL] get_dihedral for multiple files(states of a movie)

Hi Tasneem, python for state in range(1, cmd.count_states() + 1): angle = cmd.get_dihedral(58/N, 58/C, 58/CA, 58/CB, state) print state, angle python end Cheers, Thomas Tasneem Ali wrote, On 01/10/13 17:08: Hello all, I have generated a movie of 300 snapshots (MD simulation

Re: [PyMOL] apbs2 plugin failure

Hi Andreas. The line: /usr/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py shows that you are using the apbs tools from Michael G. Lerner. http://pymolwiki.org/index.php/APBS You might want to try out a little modified version of that. http://pymolwiki.org/index.php/Apbsplugin You

Re: [PyMOL] unittest for get_coordinate function

Hi Martin, I wonder, what is a most meaningful way of programmatically determining that a line of text in an arbitrary file contains atomic coordinates? The context of this question is that I plan to write a program that reads two files containing coordinates and has to perform operations on