Hi Andy! I added "in ChimeraX" to the subject line to make it more obvious to the Chimera users. We recommend sending ChimeraX questions to chimerax-users@cgl.ucsf.edu (CC'd here so you don't need to re-send) instead of chimera-users so that people don't get confused between the two programs - thanks!

Here are some thoughts on how to do it in ChimeraX:

(1) is anything in the view moving (rotation, translation, conformational change) while this model fades? If not, you can simply use "crossfade" or if you are recording a movie anyway, better to use "movie crossfade", in the script between where the model is shown and where it is hidden. https://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#crossfade

(2) if you want motions of the view or of individual models at the same time as the fading, then crossfade won't work. Instead you have to do something fancier. Instead of hiding the model you could try gradually changing its transparency from 0% to 100% over some number of frames. This requires combining the "transparency" command with a "perframe" command to iterate over different transparency levels, since you don't want to have to put in 100 (or more) transparency commands. For example, if the model is currently completely opaque (0% transparent) then you can make it completely transparent (100% transparent) over 240 image frames with something like

roll y 0.1 perframe 'transparency #7 $1 target abcsp' range 0,100 frames 240; wait 240; ~perframe

The "roll" command is only included above as an example so you can see how this fading works during motions. See the help pages for "transparency" and "perframe": https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html

However, it will require experimentation with how you specify the other commands for the motion (view, turn, roll, zoom, coordset, etc.) in your command script to make this fading happen at the same time as those motions. Even experts don't get their movie scripts right on the first try; I usually have to change and re-run my script several times. I don't even add the movie-recording commands until after I get all the motions and display changes right.

Carrying on from the example above, you can stop the roll and make the model opaque again with something like

stop transparency #7 0 target abcsp

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

On Jul 14, 2023, at 3:09 PM, Sen, Anindito via Chimera-users chimera-users@cgl.ucsf.edu wrote:

Dear Chimera X team,

Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie.

typically I use

hide #7 model

Stay safe & Regards

Anindito Sen. Ph.D

Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257

Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu