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.
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.
Thank you! It works for me. El lun, 10 mar 2025 a las 10:22, Elaine Meng (<meng@cgl.ucsf.edu>) escribió:
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.
participants (2)
-
Elaine Meng -
Gabriel López Velázquez