Hi Ale, In the future please use chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> 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 Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I'll reply to this post for my question cause the title seems appropriate. I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX.
This is the log: measure sasa /A Solvent accessible area for /A = 22276 measure sasa /A:trp & aromatic-ring Solvent accessible area for /A:trp & aromatic-ring = 1824.9 measure sasa /A:phe & aromatic-ring Solvent accessible area for /A:phe & aromatic-ring = 3339.6 measure sasa /A:tyr & aromatic-ring Solvent accessible area for /A:tyr & aromatic-ring = 3977.3
But the I tried to get the sum:
measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3
Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest.
Thank you!! Best, Ale