Hi Martin,
I do this quite often in Pymol using the pair fit menu pull down.
Wizard > Pair_fitting
You can just click on the three atom pairs you need then "fit 3 pairs". You can
highlight the residues in question as stick to make it easier.
I'm sure you can use command line too
Pair_fit 1xyz
Hi Martin,
I suggest to superpose the conformations with Theseus and use PyMOL for
visualization.
http://www.theseus3d.org/
You may also try the PyMOL command "alignto" (not available in older
PyMOL version), but I expect better results with Theseus.
Cheers,
Thomas
Martin Breugst wrote, O
Dear PyMOL users:
I want to use PyMOL to generate a nice figure showing six different
transition state structures superimposed in one single picture. I have
already tried to use the commands pair_fit, overlay, and align but I did not
get the results I have expected. Is there any way to tell PyM
Hi Francis,
Volumes require GLSL (shaders). Intel video cards (Express/HD) are
known to have issues and (typically) cannot render volumes in PyMOL.
You may appeal to Intel to improve their drivers.
One last thing -- you can try upgrading your driver and trying again.
Cheers,
-- Jason
On Thu, A
I load my .ccp4 map and try to activate volume visualization ('A' -> Volume ->
'Default').
However, pymol crashes almost immediately.
I'm using the incentive version of MacPyMOL .. version 1.4.
The hardware requirements seem to be explicitly for stereoscopic setups. Can I
get away with a n
Hello,
I have an old session file, and I would like to extract the color
information of certain objects in it. I use print
cmd.get_session()['names'] to get the scene information, but which
values in the output arrays contain the information about the color?
Thank you,
Vitaly
On Tue, Feb 21, 201
Dear Colleagues,
This is friendly but final reminder that Tuesday, April 17 is the application
deadline for the fifth annual CCP4 Summer School "From data collection to
structure refinement and beyond".
On-line application and all details about the school can be found on its web
site: http://www
