Re: [PyMOL] Molecular Visualisation in PyMol

[James S. <jms...@gm...>]

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 representation of
the conformational distribution of the selected side-chain based on
simulation data  projected on the receptors cartoon diagram - it should
looks like the alignment of the whole ensemble (in transparency view) onto
the averaged (solid-view) structure) not just a colour specter. If you know
how to do it in PyMol based on one pdb please let me know.

James

2014-09-22 10:16 GMT+02:00 Gianluca Santoni <gia...@ib...>:

> I did something similar once.
> For mainchains, you can at first calculate B-factors (similar as in
> crystallography) from md simulation, that would be added to your starting
> (or final, i don't remember) structure.
> then use the cartoon-putty representation to visualize your structure.
>
> You could try using something similar, like for exemple a color spectrum
> of b-factors,for the sidechains.
> In this case don't forget to exclude the N-ter and C-ter from your
> calculations, or they will completly flatten your spectrum.
>
> Cheers,
> Gian
>
>
>
>
> On 9/21/14 9:19 AM, James Starlight 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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>
> --
> Gianluca Santoni,
> Dynamop Group
> Institut de Biologie Structurale
> 6 rue Jules Horowitz
> 38027 Grenoble Cedex 1
> France
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