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 <jmsstarli...@gmail.com>:
> 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 Goldstone <jgoldst...@whoi.edu>:
>
>> 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" <jmsstarli...@gmail.com>
>> wrote:
>>
>>> 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 like in the
>>> molecular dynamics simulation) by introdycing of some filter on this part
>>> like some kind of bluring). Of cource I can do it by taking several aligned
>>> snapshots from MD and load it in the Pymol but here I wounder if its also
>>> possible do from one pdb structure.
>>>
>>> Thanks for help,
>>>
>>> James
>>>
>>>
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