Dear Eliane, Thank you for your help, the information you provided answered my question. The example you provided was clear and i extrapolated from it . Regards, Christian ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, March 4, 2025 6:58 PM To: FRANGIE Christian <christian.frangie@ulb.be> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Calculate residue surface area Dear Christian, I added a descriptive subject line -- this is useful for our archive. You can use "measure sasa" to measure the solvent-accessible surface area (SASA) with "setAttribute true" to assign values per residue and per atom. Then you can report the SASA for the residue(s) of interest using "info residues" -- see: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmeasure.html%23sasa&data=05%7C02%7Cchristian.frangie%40ulb.be%7Cb02dda1c6849450611e508dd5b4637ef%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638767079348254764%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=iU2LS9rzeFzQZlIRIPjZr2QDmUdpuHzxW%2BNBIaFaeLI%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Finfo.html%23residues&data=05%7C02%7Cchristian.frangie%40ulb.be%7Cb02dda1c6849450611e508dd5b4637ef%7C30a5145e75bd4212bb028ff9c0ea4ae9%7C0%7C0%7C638767079348275063%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aYbeAs3pWtnCWyfXSsTBUQBeKeQXX2ed6J9vBZGnA7k%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues>> The main thing is to be very careful what atoms you specify in the "measure sasa" command. If you just give the whole model, for example, it would include the solvent into the same surface as the protein. So you may want to include the specifier "protein" in the command. Example: open 2gbp measure sasa #1 & protein info residues /A:150 attribute area This reports the value in the Log. There is also an "info residues" option to save to text file instead, if that's what you want. You can specify the whole protein to list all the residues, e.g. info residues #1 & protein attribute area 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 4, 2025, at 1:51 AM, FRANGIE Christian via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF ChimeraX Support Team,
My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter?
Warm Regards, Christian
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