Hello Jessica, Instead of crossfade (which does not allow motions at the same time), you could try using the "perframe" command to apply a gradual change with an embedded "transparency" command. E.g. for simultaneous rocking and fading, commands: open 1zik rock y 50 272 cycle 136; perframe "transparency #1/A $1 target r" range 0,100 frames 272; wait 272; ~perframe ... where the rock command through the ~perframe command should all be on one line separated by semicolons (although the mail-message processing may break it up into multiple lines). Help pages for the various commands with options, syntax, examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rock.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.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 May 9, 2022, at 2:28 PM, Rabuck-Gibbons, Jessica via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello, Would there be a way to apply crossfade ust one part of the model while making a movie? For example, I’m trying to make a movie of several different ligands in one protein. In Chimera, I can show or hide the ligands over a certain number of frames, but this functionality doesn’t seem to exist in ChimeraX. Crossfade is the closest command, but it crossfades the rocking motion as well as the show and hide motion. Is there a way to get around this? Thanks, Jessica