Hi Dennis, The molecular surface calculation method in ChimeraX is different than in Chimera. However, ChimeraX also has a probeRadius parameter, as well as a gridSpacing parameter that affects the resulting vertex density. See the "surface" command documentation for these command-line options:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options
There are several export formats that include surface vertex positions. Take a look at the "save" command (or menu File... Save) and see if one of those meets your needs, namely the "3D objects" output formats listed near the bottom of this table: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats
"save" command https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.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 Sep 30, 2023, at 2:14 PM, Dennis Dannecker via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I would like to ask a question regarding the surface representation of protein molecules in ChimeraX.
I remember from Chimera that one could very customize the surface representation in terms of probe size, vertices density, and dot size used in the dot surface representation. While ChimeraX also allows to show dot surface representation, does it also allow for setting these attributes?
But the more important question of mine is, can one export/extract the coordinates (spherical or cartesian) of the dots generated during dot surface representation. I would be interested in a file that holds the coordinates of these dots/particles around the molecule. In principal that should be possible, but as always, how amenable is that data?
Thank you very much. Cheers Dennis