Hi Gabriel, You could use the "perframe" command to run "measure sasa" at every frame of the MD during playback with the "coordset" command. See command help pages for options and details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> Here is my example trajectory of 80 frames, opened using command: open 1plx coord true Then I can play the trajectory back with the "coordset" command and measure sasa at every step with the following. Be careful what atoms you specify with "measure sasa" -- if you just use model number it will include solvent, ligands, etc. Probably you only want the protein, as in my example commands: perframe "measure sasa protein" range 1,80; coordset #1 1,80 ... then there would be 80 lines in the Log with the SASA values. You would have to save the Log to a file (e.g. command "log save") and reformat for your favorite graphing program, as there is no feature to do that inside of ChimeraX currently. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save> 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 Mar 10, 2025, at 9:01 AM, Gabriel López Velázquez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, I am sorry; I did not state the subject of my previous email.
I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.