Thanks Elaine for the reply. This is causing me some trouble because I’m trying to use Chimera in a script. It sounds as if - when Chimera opens mmCIF files and saves in PDB format, the numbering may change and there’s not a way to get the new numbering - but when I repeatedly save mmCIF files, Chimera crashes (I submitted a bug report earlier today) Best, Daniel
On Apr 25, 2024, at 4:15 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Daniel, Alphafold fetch is in mmcif format only. I guess that the Alphafold database does not provide multiple formats.
You can see this from the info given in the Log with command "open formats" and in the fetch-sources table in the HTML docs: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch-table>
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 Apr 25, 2024, at 3:50 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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