Hi Gian,
thank you very much! The idea to associate side chain dynamics with the its
B-factor is very attractive for me! However I'm not sure how to make
ensemble-like view of the side chains in accordance to its B-factors - in
fact as the end of the day (night?!) I'd like to obtain representatio
I should to specify that I ask this because normally VMD didn't produce
multi-state pdb from the md trajectory so it seems I need to use some
plugin to load *.dcd or *.trr
James
2014-09-22 13:53 GMT+04:00 James Starlight :
> Hi Jed,
>
> so this method is working of the ensemble of the pdb files
Hi Jed,
so this method is working of the ensemble of the pdb files taken from the
MD simulation or NMR structure, isnt it? Could someone explain me step by
step how to obtain such inputs for the PyMol (from the step when I've load
my trajectory to the VMD).
James
2014-09-21 20:42 GMT+04:00 Jed G
You could extract the flexible residues into one multistate object and use
show all_states. So, you'd only be dealing with 2 objects - Ca and residues.
Jed
On Sep 21, 2014 3:23 AM, "James Starlight" wrote:
> Dear Pymol users!
>
>
> In this topic I've decide to put all questions regarding visuali
Dear Pymol users!
In this topic I've decide to put all questions regarding visualisation.
This time I'm very intresting whether it possible to add some effect of the
"flexebility" or "ensemble-like dynamics" on the selected elements (e.g
selected side-chains to convey a sense of its flexibility
