[chimerax-users] atom serial_number is inconsistent with PDB serial numbers in multi-chain structure

Hi all,

I’ve been debugging an off-by one error in a ChimeraX script I’m working on, which I’ve traced to a apparent inconsistency between the serial_number reported by ChimeraX for an atom and the actual serial number of that atom read/written in PDB format.

To reproduce: open 5MJ7 select #1/B:6@CA info atoms sel attribute serial_number

==> atom id /B:6@CA serial_number 2548

but the correct serial number for this atom in 5MJ7.pdb is 2549.

Maybe this is because the TER record for chain A takes up one serial number in the PDB file, but ChimeraX doesn’t include it as a numbered atom?

Regardless, how can I query ChimeraX for the actual serial number that will be written if I write out a PDB file?

Thanks, Daniel