[Chimera-users] animation commands in a morph movie

[Elaine Meng]

Hi Natesh,
I guess you are trying to move the ligand at the same time as showing the morph.  

Remember, the MD Movie per-frame scripting is mostly for commands you want to do at EVERY step of the trajectory.  You should only save the bound and unbound positions of the ligand once, not using the per-frame scripting, just typing the commands into the command line, and then move the ligand to the unbound position.

Then, your reset to bound position would be in the per-frame script:
Yes, there is a mechanism to execute only at a specific frame using the MD Movie per-frame scripts, which is actually explained in the text on the dialog: “Commands prefixed with #N: will be executed at frame N” so maybe something like:

#20: reset p1 50

… to start resetting at frame 20 of the morph trajectory.  However, I haven’t tried this for starting multi-frame actions.  I’ve only tried it for single-frame actions like coloring something or calculating H-bonds.   

If that doesn’t work, it may make more sense to just script the whole thing, not using MD Movie.  The coordset command plays back trajectories, for example.  See this tutorial for scripting a movie where the ligand flies into the binding site and then the protein morphs (not at the same time, though):

<https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html>

With this separate scripting approach, you can also put more time before and after playing the morph with “wait” commands, add titles (“2dlabels”), rotate the view, etc.

More examples of movie scripts that include morphing:

FGFR1 kinase activation
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>

Ball-and-socket motion
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>

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

> On May 31, 2019, at 5:21 AM, Natesh Singh <natesh.singh at univ-lille.fr> wrote:
> 
> Dear Chimera development team,
> 
> I am trying to add a simple animation into the morphed trajectory that was developed using two unique conformations (protein and proten-ligand complex). I want the ligand to fly into the binding site (of course ligand is not considered in the morph since it was not a part of a chain), but I guess this could be done.
> 
> contents of my model panel.
> ID 0 ligand surface
> ID 0 conformation A (protein-ligand complex)
> ID 1 conformation B (protein)
> ID 2 Morph (400 frames)
> 
> I am adding the following commands into the perframe box of md movie:
> 
> # Save bound view.
> savepos p1
> 
> # Move ligand away and save unbound view.
> move y -10 model #0 ; turn z -30 model #0 center #0
> scale 0.2
> savepos p2
> 
> #fly ligand into the binding site
> reset p1 100
> wait
> 
> But it's not working the way I want. I just want the ligand to fly slowly into its original position may be within 25-50 frames.
> Could we execute the commands at a specific frame number? Kindly let me know what would be the correct commands to achieve this effect.
> 
> Many thanks for your help.
> Sincerely,
> Natesh
> University of Lille