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
Hi Pete,
Versions of PyMOL before v1.5 will not be able to properly read maps
in session files written by PyMOL v1.5 and later. We updated the map
code to enable visualization of data beyond the unit cell, and added
some new functions that allow you to copy symmetry and space group
information fro
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 mi
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 simulat
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
---
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
wrote:
> Hi,
> I recently upgraded my desktop to Ubuntu 12.10.
>
> When I load a pdb in py
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
>
Hi Robert,
you again need to set the "surface_color" for the selected residues,
instead of using the color command. That these two are not synced makes
sense, you can for example have a half-transparent surface in one color
and a stick representation below in another color.
PyMOL> set surface_col
