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