Hi Elaine !
Today I tried to play with movie crossfade to include this transparency effect between frames but it did not work . Where the command should be actually added ( e.g. inside the movie record … wait x or alternatively after recording and before recording)?
Should I add it for each frame in a loop or there is a more automatic solution e.g to apply it like a filter effect when I record movie using coordset ?
Thank you very much in advance!
Enrico
Hi Enrico,
Crossfade does not do any movements, it is only like making one image fade (gets more and more transparent) when the next one fades in (gets more and more opaque).
coordset #1 96
crossfade 60; coordset #1 95; wait 60
The "crossfade" help has more examples
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html>
There is another command "movie crossfade" that gives basically the same result but is only for when you are recording a movie, since it does not show the crossfade in the graphics window. So you can use that if you want, you just can't see it "live"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade>
If you meant actually moving the atoms gradually, you could try morphing from each position to the next position. However, you cannot do it with the trajectory, you would need to save the ligand docking ensemble as a multi-model pdb if you don't already have it, then reopen it (then you'd have something like #1.1, #1.2 .... #1.96), and then morph from each one to the next, something like
morph #1.1-96
.... of course there are adjustable parameters to morph, see options in the help
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jan 27, 2025, at 5:03 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users!
>
> I am recording a short animation demonstrating my docking ensemble
>
> # start recording
> movie record
>
> ## play DOCKING movie from end to begining
> coordset #1 96,1,-1
> wait 96
>
> Would it be possible to add a smooth transition between each frame (docking pose) using the movie crossfade command ? If so, how should this command be placed in the script ?
>
> Many thanks in advance !
>
> Enrico
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