[chimerax-users] video of digestion kinetics

[Elaine Meng]

Hi Tynan,
I'm not sure if you meant to send this to the chimera-users at cgl.ucsf.edu list or the chimerax-users at cgl.ucsf.edu list.  Anyway, using either program, UCSF Chimera or UCSF ChimeraX, in general you would need to make a command file for what happens during the movie.  The command file could include hide successive parts of the peptide, i.e. if residues 10-12 get cut off first, hide them, then several steps (movie frames) later hide the next set of residues to get cut off, etc.

In either program, making a command script would require learning the commands, so you would need to invest some time.  In Chimera, however, there is also a graphical interface to movie recording, so if you are able to use the menus instead of commands to get to various states you want in your movie (e.g. with more and more of the peptide hidden), with this Movie Recorder interface you can save them as scenes and place them on a timeline.  Still, however, at a minimum it will require learning how to use the menus of Chimera to do all the coloring, styles, 2D labels etc. that you want in your movie.  

ChimeraX "making movies" page:
<https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>

Chimera "making movies" page:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html>
Chimera Movie Recorder tool:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 18, 2021, at 10:32 AM, Tynan A. Becker <tabecker at alaska.edu> wrote:
> 
> Good morning, 
> I have kinetics data from the in vitro digestion of a protein by several enzymes.  For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points).  I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides.  Looking online, I see that you have some videos with proteins showing alternate conformations.  Do you think it possible for me to show the cleavage sites that develop sequentially over time in a specific protein as it is digested?
> Thanks, 
> Tynan