Dear Suhas, I hope your week is great as well, and we're glad you like ChimeraX! We recommend sending ChimeraX questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless they include private data. That way others can also answer, or benefit from the answers. In this case, it is explained in the "measure sasa" help. Please see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> The command measures the surface area *enclosing* the specified atoms. That is different than the surface area of those atoms in the context of the larger structure. So when you give two commands measuring two parts you also get more surface that goes around the ends of those parts. If you wanted the SASA in the context of the whole protein or whole chain, you would have to do it differently. As explained in the help link above, if you want to measure the SASA of those parts in the context of the whole protein chain's surface, it would instead be something like measure sasa /A sum /A:1-10 measure sasa /A sum /A:11-20 measure sasa /A sum /A:1-20 The Log gives: measure sasa /A sum /A:1-10Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-10 (66 atoms) of /A (2615 atoms) = 1143 measure sasa /A sum /A:11-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:11-20 (80 atoms) of /A (2615 atoms) = 427.09 measure sasa /A sum /A:1-20Solvent accessible area for /A (2615 atoms) = 28035 Solvent accessible area for /A:1-20 (146 atoms) of /A (2615 atoms) = 1570.1 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 Jul 23, 2024, at 11:59 PM, Suhas Srinivasan <suhas.srinivasan@stanford.edu> wrote:
Dear Dr. Meng,
Hope you are having a great week!
Thank you for developing and maintaining ChimeraX as an essential analytical software for the community.
We had a query since we noticed a discrepancy in the way SASA is reported. If you were to consider the AlphaFold database structure for PCBP1 (Q15365) and perform the below SASA measurements, we noticed that: SASA(1 to 10) + SASA(11 to 20) ≠ SASA(1 to 20)
measure sasa /A:1-10 Solvent accessible area for /A:1-10 (66 atoms) = 1385.3 measure sasa /A:11-20 Solvent accessible area for /A:11-20 (80 atoms) = 1632.6 measure sasa /A:1-20 Solvent accessible area for /A:1-20 (146 atoms) = 2850.8
There is a difference of ~167 sq. A. It would be very helpful to understand why such a large difference exists when considering contiguous sequences of atoms/residues.
ChimeraX-1.8 macOS-14.5 (Intel)
Thank you for your consideration.
Kind regards, Suhas Srinivasan