[chimerax-users] video of digestion kinetics

[Elaine Meng]

Hi Tynan,

Besides abruptly hiding atoms and bonds, you could fade them in or out over time (spread hiding across multiple movie frames), or don't hide them but select them (shown as green outline), or color them differently, or show them with different styling like fatter or thinner sticks, etc.  These are all things you can do with the commands of either program, normal stuff that people frequently do when making figures or movies.

Or instead of (or in addition to) changing how the peptide is shown, you could show a 2D label that is an arrow pointing to the cleavage point (see 2dlabels command of either program).

Elaine

> On Jan 18, 2021, at 12:04 PM, Tynan A. Becker <tabecker at alaska.edu> wrote:
> 
> Hi Elaine, 
> Thank you for the very quick response.  The info does help.  I was thinking that I might be able to take this approach.  And I don't mind learning the command line 
> 
> However, I was also wondering if there was a way to highlight the peptide bonds between residues to show the actual cleavage points and what gets added as time goes on.  This would be a more accurate representation of my data because some peptides are "lost" due to limitations in mass spec rather than the digestion (a very short peptide might not have been digested, but also wasn't IDed by the instrument).
> Thank you!
> Tynan
> 
> -------- Forwarded Message --------
> Subject:	Re: [chimerax-users] video of digestion kinetics
> Date:	Mon, 18 Jan 2021 11:47:07 -0800
> From:	Elaine Meng <meng at cgl.ucsf.edu>
> Reply-To:	ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> To:	Tynan A. Becker <tabecker at alaska.edu>
> CC:	chimerax-users at cgl.ucsf.edu
> 
> 
> 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
>