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:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>

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 <chimerax-users@cgl.ucsf.edu> 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