ChimeraX knows which atom every surface vertex is associated with. But if you just want the solvent accessible surface area per atom then use the "measure sasa" command as Elaine suggested. The per-atom area calculation does not use the displayed triangles. Instead it does an analytic calculation that is described here https://www.cgl.ucsf.edu/chimera/data/sasa-nov2013/sasa.html The MSMS solvent excluded surface calculation in Chimera failed on many large atomic models (> 10,000 atoms) so we replaced it with a grid based solvent excluded surface algorithm which reliably computes surfaces for any size atomic model. Tom
On Oct 19, 2023, at 9:55 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dennis, If you use the "measure sasa" command in ChimeraX, you can assign SASA values per atom and residue as attributes named "area":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
Attributes can be used for specification, coloring, etc., and written to a file with "save"
<https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
SESA is not available, however. ChimeraX does use a different method than Chimera to calculate the molecular surface, much more robust (less prone to failures).
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 19, 2023, at 4:33 AM, Dennis Dannecker via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Chimera/ChimeraX team
I recently asked already a question regarding the saving/exporting of vertices generated during the surface calculation in ChimeraX and the associated parameters with this surface generation.
On a related note, I wanted to ask whether it is possible to also extract the surface (SESA and/or SASA) on a per atom basis. MSMS calculates not only the vertices for each atom (usually several vertices per atom) but it also calculates the SESA and SASA on a per atom basis. Now, I was wondering whether something is possible in ChimeraX too. As I was parsing through the docs, I was wondering whether ChimeraX calculates the surface no longer using MSMS. The vertices density supported by ChimeraX is considerably higher than what I can get with my standalone MSMS program (at least factor 6). So, if ChimeraX does not longer employ MSMS, what else does it use?
With "measure convexity" I get the surface vertex positions, normals, convexity values, and triangles. Unfortunately, the association with the corresponding residue is lost (however, can be regained with a little bit of work I guess, simply using euclidean distance).
Question: Is there something similar for the SESA or SASA of the different atoms in the model/chain. In theory, this information should be available, at least the SESA. I am just wondering whether there is a way to write this out as a raw txt file in ChimeraX
The closest I found in the save command is the .obj or .vtk format. However, both are semi-satisfying in that that they both do not provide the data looked for and are in somewhat special formats, at least the vtk. The .obj file is much much bigger than what MSMS or "measure convexity" generates, and not really handy for then working with the data in other programs, mainly python.
As always, I very much appreciate any help and wish to thank the team for their contributions to the field.
Best regards
Dennis
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