Dear Sir/Madam, I am Nikhita, an undergraduate student working on a research project and I am considering to use ChimeraX to calculate solvent accessibility surface area (SASA) for some residues of a protein. However, since I would like to calculate relative solvent accessibility surface area manually, I am using the reference maximum SASA values from Tien et. al. (2013) which mentions that using softwares that calculate SASA using the Lee & Richards method are preferable. As such, I would like to ask if ChimeraX uses the Lee & Richards method to calculate SASA as I could not find much about this on the ChimeraX website. Thank you! Warm regards, Nikhita
Hi Nikhita, ChimeraX uses a standard analytical calculation of solvent accessible surface area. I don't know if it is the Lee and Richards method. I wrote the ChimeraX code for this and a description of it is here. https://www.cgl.ucsf.edu/chimera/data/sasa-nov2013/sasa.html It computes the exact areas of the spherical polygons that make up the solvent accessible surface. It shouldn't matter what the calculation method is if it is an exact (rather than approximate) method. But what will matter and will surely be a problem is that the area values depend on the atom radii, and everyone uses different atom radii. So your reference residue areas will be with whatever atom radii those authors decided to use and won't be the same as ChimeraX atom radii. ChimeraX atom radii are described here https://www.cgl.ucsf.edu/chimerax/docs/user/radii.html Tom
On Jun 15, 2025, at 9:44 PM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam,
I am Nikhita, an undergraduate student working on a research project and I am considering to use ChimeraX to calculate solvent accessibility surface area (SASA) for some residues of a protein. However, since I would like to calculate relative solvent accessibility surface area manually, I am using the reference maximum SASA values from Tien et. al. (2013) which mentions that using softwares that calculate SASA using the Lee & Richards method are preferable. As such, I would like to ask if ChimeraX uses the Lee & Richards method to calculate SASA as I could not find much about this on the ChimeraX website. Thank you!
Warm regards, Nikhita _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Tom, Thank you so much for your reply! I checked through the atom radii used by the authors of Tien et. al. (2013) paper and it was slightly different from the ChimeraX atom radii. Hence, I was just wondering if a slight difference would really make the calculation of relative solvent accessibility surface area inaccurate. Thank you! Warm regards, Nikhita
Dear Tom, I would also like to check if there is a way to directly calculate relative solvent accessibility surface area via ChimeraX instead of manually comparing SASA with reference values from a separate paper and perhaps this would also make it a more accurate method of obtaining relative SASA? Thank you! Warm regards, Nikhita
HI Nikhita, One possibility is to try to change to the same radii as that paper used before calculating SASA in ChimeraX. It depends whether they give the full information of what radii they used, and how much work you are willing to do (how many ChimeraX "size" commands) to make the ChimeraX radii the same. ChimeraX "size" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> The other possibility is also a lot of work. You'd have to create all the reference states (something like extended Gly-X-Gly tripeptides is what some people have used, where X is each of the 20 standard types of residue) and measure the SASA of the "X" residue in each one in ChimeraX as a representative of the exposed area of that residue type. Then you would have your own set of reference values using the ChimeraX radii. 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 Jun 16, 2025, at 9:12 PM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Tom,
I would also like to check if there is a way to directly calculate relative solvent accessibility surface area via ChimeraX instead of manually comparing SASA with reference values from a separate paper and perhaps this would also make it a more accurate method of obtaining relative SASA?
Thank you!
Warm regards, Nikhita _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Elaine, Thank you for your reply! May I ask how the reference states (ie. the extended Gly-X-Gly tripeptides) are created in ChimeraX? Thank you so much! Warm regards, Nikhita
Hi Nikhita, You could use the "peptide" option in the Start Structure section of the Build Structure <https://www.cgl.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> tool to create Gly-X-Gly peptides, but if you're creating a lot of them it might be faster/easier to use the "build start peptide" <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/build.html> command to create the peptides. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 17, 2025, at 8:27 AM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you for your reply! May I ask how the reference states (ie. the extended Gly-X-Gly tripeptides) are created in ChimeraX?
Thank you so much!
Warm regards, Nikhita _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Eric, Thank you for your reply! I would also like to ask when I begin to Build Structure and create Gly-X-Gly peptides, there are multiple parameters that I could adjust such as Φ/Ψ with values for alpha helix/anti parallel beta strand/parallel beta strand/310 helix/pi helix and the rotamer library. I was wondering if just using the default values would be accurate enough? Could I also check when I measure SASA for the tripeptides, do I use the measure sasa /A:2 command or the info residues attribute area command as both give a different SASA value but from my understanding, the info residues attribute area gives a SASA value that represents the exposed area of the residue within the whole surface of the tripeptide while measure sasa command gives a SASA value that is representative of the area of that residue alone and hence, using info residues attribute area to obtain the reference SASA values is more accurate? Thank you so much! Warm regards, Nikhita
Hi Nikhita, You should decide for yourself which angles you think are best for "extended." My guess is you could just use 180 and 180, which would be similar to the beta-strand options. When you "measure sasa /A:2" that draws a surface around only the one residue and measures its surface area. However, that's not what you want. Instead you want the area of the residue but in the surface drawn around the whole tripeptide. So if the tripeptide were all of #1 you would use something like "measure sasa #1 sum #1/A:2" ... see the help for "measure sasa" which explains all this: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> ...or (essentially the same process, see the help above) use "measure sasa #2 setAttribute true" to generate the whole tripeptide surface area with residue area assignments and then use "info residues" command to get the "area" value of the residue in the tripeptide. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> 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 Jun 17, 2025, at 8:45 PM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Eric,
Thank you for your reply! I would also like to ask when I begin to Build Structure and create Gly-X-Gly peptides, there are multiple parameters that I could adjust such as Φ/Ψ with values for alpha helix/anti parallel beta strand/parallel beta strand/310 helix/pi helix and the rotamer library. I was wondering if just using the default values would be accurate enough?
Could I also check when I measure SASA for the tripeptides, do I use the measure sasa /A:2 command or the info residues attribute area command as both give a different SASA value but from my understanding, the info residues attribute area gives a SASA value that represents the exposed area of the residue within the whole surface of the tripeptide while measure sasa command gives a SASA value that is representative of the area of that residue alone and hence, using info residues attribute area to obtain the reference SASA values is more accurate?
Thank you so much!
Warm regards, Nikhita
participants (4)
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Elaine Meng -
Eric Pettersen -
komatireddy.nikhita＠gmail.com -
Tom Goddard