[Chimera-users] Dynamic Protein

[Alex Nazlidis]

This is great, thank you so much for the info Elaine!

Kind regards,
Alex


Στις Πέμ, 25 Οκτ 2018 στις 8:49 μ.μ., ο/η Elaine Meng <meng at cgl.ucsf.edu>
έγραψε:

> Dear Alex,
> Oooh,  Ken Dill, one of my favorite professors!
>
> Short answer is you can certainly create movies of trajectories
> (conformational changes through time), but generally those trajectories are
> calculated some other program, and you can’t simulate protein folding.
>
> For folding or any other major conformational changes, the hard part would
> be calculating the trajectory, which Chimera will NOT do for you.  Chimera
> can create “morph” trajectories which are fairly simple interpolations
> between endpoint structures.  However, they are not biophysically accurate
> calculations of the paths the atoms would really take; instead they are
> meant to help people understand conformational differences between two
> states, which are generally not as extremely different as unfolded and
> folded.  You can give it several intermediate states and then morph
> piecewise between them (A->B, B->C, C->D etc.), but you’d still to generate
> all of the input conformations somehow.
>
> Chimera Morph Conformations tool
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
> >
> … examples of use in these tutorials
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
> >
>
> Chimera does have a Molecular Dynamics Simulation (trajectory calculation)
> tool but it is somewhat limited and slow compared to dedicated MM/MD
> software packages.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
>
> If you had calculated the trajectory using some separate software
> (remaining agnostic as to how you’d actually do that), if it were in one of
> the several standard formats that Chimera understands, you could read it
> into Chimera and “play” it back with the MD Movie tool.  In Chimera you can
> control the colors, display styles, etc., add 2D labels/titles, and record
> the trajectory as a movie.
>
> MD Movie tool  or  “coordset” command for trajectory playback
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
>
> Making movies
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
>
> I hope this clarifies the situation,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 25, 2018, at 10:27 AM, Alex Nazlidis <nazlidisalex at gmail.com>
> wrote:
> >
> > Dear Elaine,
> >
> > is there any way in chimera to produce a clip similiar to this (
> https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating
> the dynamic nature of a protein and its folding process.
> >
> > Thank you very much in advance,
> > Alex
>
>
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