[chimerax-users] Morphing structures with ligands (glycans)

[Elaine Meng]

Hello Nebojša,
Glad you figured out how to include the glycans without too much trouble!

The ways to make the movie longer are to either increase the number of movie frames or change the movie playback frame rate.

One way to increase the number of movie frames is to increase the number of frames in each morph section of the trajectory. This is done with "morph" command option "frames N" where N is the number, default 50:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>

I don't know how you are recording the movie.  If you just use the red record button on the slider it does not allow you to set options, but simply uses "movie record" and "movie encode" with "framerate 25.0".  I think I had suggested in a ticket that it should instead open a movie-recording dialog to allow people to change those options, but it has not been done.  

So if you want to specify a slower movie framerate, you will need to use commands yourself, including "coordset" to play back the trajectory.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>

E.g. if trajectory is #3 and has 51 frames, something like

movie record; coordset #3 1,51; wait 51; movie encode ~/Desktop/movie.mp4 framerate 20

Also if you are using commands you have more freedom to do what you want in the movie, like play the whole thing back and forth 5 times if you wanted by using more "coordset" commands, and add more wait frames at the beginning and end if you want it to be still for a while before and after morphing.

See also the "making movies" page and links therein to useful commands and movie tutorials:
<https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>

I hope this helps,
Elaine

> On Dec 13, 2022, at 1:33 PM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello Elaine,
> 
> Thank you so much. I managed to take care of the atom IDs and everything works now. I was wondering if you could give me an example of how to increase the length of the movie or change the number of frames. My structures look great, but the movie seems to be playing too fast
> 
> Thank you once again.
> 
> Best regards,
> Nebojša Bogdanović, Ph.D
> Department of Physiology and Biophysics,
> School of Medicine,
> Case Western Reserve University
> 
> 
> On Tue, Dec 13, 2022 at 4:08 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Nebojša,
> There are some rules about whether the nonprotein atoms will be included in the morph trajectory, listed here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>
> 
> I will try to summarize here:
> 
> (1) Only atoms common to all of the input structures are included in the morph trajectory. This is probably the issue.  Maybe some of your structures don't have the glycosylations or they are shorter or different between the different structures.  It is OK for the proteins to have different sequences as long as they are similar enough to sequence-align, but where the sidechains are different only the backbone will be included in the final morph.
> 
> (2) HET residues such as ligands and ions are only included if at least one of the following applies:
>         • the entire atomic models have identical sets of atoms with the same atom names, residue numbers, and chain IDs
>         • you use command option "same true" and the HET residues in question are present in all of the input structures with the same atom names, residue names, residue numbers, and chain IDs (even if other atoms are different)
>         • the HET residues are bonded to the paired chains either directly or indirectly through other paired HET residues
> 
> #2 is probably satisfied because the glycosylations are covalently bonded to the proteins, but #1 is probably not satisfied.  You could try to add atoms to (or delete atoms from) the individual input structures to meet #1, but depending on how large the differences, this is likely to be difficult.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Dec 13, 2022, at 12:45 PM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hello,
> > I am looking into morphing several protein structures that contain glycans important form the function. The structures are all the same protein, in different states so the sequence info is good. Is there any function that retains the glycans visible once the command morph #1-5 same true produces a new model? I can just show them from origin structures but this does not look the best.
> > 
> > Thank you and best regards
> > 
> > Nebojša Bogdanović, Ph.D
> > Department of Physiology and Biophysics,
> > School of Medicine,
> > Case Western Reserve University
> 
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