Il 15.01.2025 18:53 Elaine Meng ha scritto:

Hi Saverio,
The points are added as fake atoms, so you can get any/all of their coordinates in the same ways used for normal atoms, such as with:

(a) "getcrd" command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/getcrd.html>

(b) saving to file, e.g. a PDB file
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

... or you can compute their centroid directly with the "define centroid" command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#centroid>

For any of these commands/actions you could use the model number of the cavity, which you can see in the cavity list dialog or in the Models panel, or you could select specific points with the mouse (although I can imagine that might be difficult).

Example:
open 2gbp
kvfinder
define centroid #1.2.3 color yellow radius 1.0

.... which would report centroid coordinates in the Log

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 Jan 15, 2025, at 7:46 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/