Sorry no, I can't think of anything like that already available in Chimera. The most similar thing is to simply calculate the surface area of some atom(s) but that does not directly measure shape, nor does it include changes in position. You may need to develop your own custom code. 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 24, 2024, at 4:03 AM, valerio chiarini via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
I'm trying to come up with some method to compare surfaces of the same protein area over some trajectory. A simple RMSF doesn't cover the analysis as a roto-traslation of some parts might retain the surface form and shape, whereas a residue might have a complete rearrangement of its surrounding without undergoing large RMSF changes. Some software based on Masif are available, tough they do not confront between trj frames.
Are there any turnarounds in chimera to do this? A function similar to RMSD but for surfaces that maybe could be emplyed in this specific case?
Thank you all,
Valerio Chiarini