Thanks Eric! What about the command alphafold fetch Which format does that open? It doesn’t seem to have the format option available. Daniel
On Apr 25, 2024, at 3:14 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Daniel,
On Apr 25, 2024, at 12:44 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.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
The default is to open a PDB entry from its mmCIF-format file. To open from its PDB-format file, the command would need to be: open 5MJ7 format pdb
select #1/B:6@CA info atoms sel attribute serial_number
==> atom id /B:6@CA serial_number 2548
When opened from the PDB-format file, the above command reports:
atom id /B:6@CA serial_number 2549
--Eric
Eric Pettersen UCSF Computer Graphics Lab
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
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