Il 13.05.2025 18:18 Elaine Meng ha scritto:

Hi Saverio,
They are just atoms, it is the same for any atoms.  You can use atom name, residue number, chain ID (if it has a chain), model number.  When you are doing this I don't know what other residues/models you have at the same time so I can't write all your commands for you, but there is nothing special.  I don't think you need serial numbers since the atom names are probably unique per residue and model.  I.e. you may also need to give residue name or number and model number if there are other residues or models with the same atom names.

If you don't know the atom names, you can label the structure, e.g.

open /Users/meng/Desktop/DB09074_vina_sf__docked_first_pose.sdf
label #1 atoms
select #1@O1
pbond #1@O1 #1@F1

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 13, 2025, at 1:58 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: 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