Hi Elaine, many thanks. Saverio 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