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 ----- 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 May 14, 2025, at 7:02 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
HI, I want to draw a pseudobond between a real atom and the centroid of six carbon atoms. How it is possible define a virtual or pseudo atom with the coordinates of the centroid as one of the ends of the psudobond?
Thanks.
Saverio
