Hello Elaine,

thank you very much for your help, pointing me to the respective tools.

Indeed, I were able to extract the vertices by exporting the .obj file. It holds a tone of information (small to medium sized protein produced a 1.5 GB .obj) which makes it a bit difficult to handle, but otherwise I think I got what I was looking for, thank you again.

Cheers
Dennis


Quoting Elaine Meng <meng@cgl.ucsf.edu>:

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.
CheersDennis