Hi Nick,
I recently was playing with (aka learning) the crystallographic symmetry
information in PDB files and now took your feature request as an
exercise. See attached file, hope it does what you had in mind.
Cheers,
Thomas
On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote:
It would be
Dear pyMol users,
I am developing a python script for pyMol. If a user clicks File-Run
and selects the script (for example c:/test/myScript.py), how do I
determine the path of the script, i.e. (c:/test/) from inside the
running script?
I tried various python possibilities
Hi Thomas,
thanks!
I noticed a few things:
- when I run supercell 2, 1, 1 I get another cell outline along the a
axis, but no atoms are shown in the second cell. Do I have to run another
command for them to show up?
- when I run the command again with other values for a, b, or c, nothing
Petr,
This is a cool problem treading on the grounds of PyMO/Python/System
integration. You could create a wrapper function that takes the
absolute path to the file, then chdir to the directory with the file,
and import the file. Once you os.chdir somewhere, cmd.pwd() should
return the new
Hi All Pymol users
I have a set of 40 X-ray
crystallographic structures complexed with inhibitors belonging to a
specific family of kinases. Binding site residues within 5 angstrom
from the inhibitor were selected for each PDB
Hi Jason,
Sorry for taking that long to answer you, I was out of town.
Well the picture that I have has 1441X814 pixels, which is way below your
4000X4000 pixels. I don't believe the resolution is the issue here but the
complexity of the scene - I am trying to ray four big proteins (the complex
Hi Renuka,
With a little bit of Python programming and better understanding of
structure alignment in PyMOL you should be able to complete your task.
First, check out the structure alignment category on the PyMOLWiki (
http://www.pymolwiki.org/index.php/Category:Structure_Alignment). Read the
Lucas,
If you'd like, please send me your session file and I can take a look
at ray tracing it or making it possible for you to ray trace it. I
did a small study a few years ago and found that if you can
hide/remove atoms for PyMOL that won't make a difference in the scene,
that could help you
rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val =
