OK, it seems like a (the?) solution to this is to read/write in mmCIF format which doesn’t have TER entries.
On Apr 25, 2024, at 12:43 PM, Daniel David Richman <ddrichma@stanford.edu> wrote:
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