[Chimera-users] Dynamic Protein

[Elaine Meng]

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