Hi Elaine, thanks for your help. I'm trying to visualize some detected interactions between receptor residues and a docked igand atoms using the pbond command. For the docked ligand I have the sdf procuded by meeko from a pdbqt or dlg file. I first load the pdb of the receptor and then the sdf of the docked ligand. How do I can make the atom specification for an element of the loaded sdf docked ligand? Thanks. Saverio Il 12.05.2025 22:44 Elaine Meng ha scritto:
Hi Saverio, You can use the atom attribute named serial_number to specify the atom in the command lind. The symbol for atom attribute is @@ as mentioned in the specification help page:
For example, to select atom number 2823 in model 1:
select #1@@serial_number=2823
I don't think you need the chain ID since the serial number should be unique per model, but it should be OK if you also include it.
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 12, 2025, at 1:26 PM, saverio via ChimeraX-users wrote: Hi, I would like to use pbond with a pair of atoms. For one of these it is available the model number , the chain ID and the atom serial number. How it is possible to give the atom specification ,having the previous three information, for using it in pbond? Thanks. Saverio