Il 14.05.2025 17:53 Elaine Meng ha scritto:

Hi Saverio,
The centroid is already a virtual atom.  So you can just draw the pbond directly to it.  When you use "define centroid" or the Axes/Planes/Centroids tool, the model number of the object is shown in the tool -- since there is only one atom in the centroid model, you can just use model number to specify it.

Example commands (create centroid model #1.2, as shown in the Axes/Planes/Centroids dialog, and draw pbond to lysine 92 NZ):

open 2gbp
define centroid ligand radius 0.8 color magenta
pbond #1.2 #1/A:92@NZ

Screenshot is below.
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco