Add option to fetch emdb map when opening a PDB structure

[Samuel.Haysom@…]

Begin forwarded message:

From: Samuel Haysom via ChimeraX-users
Subject: [chimerax-users] Is there a way to download a pdb and it's associated density map in one command
Date: September 24, 2025 at 2:45:57 AM PDT
To: ChimeraX Users Help
Reply-To: Samuel Haysom

Is there any way I can fetch a pdb file from the web (e.g. $ open 1X2Y) and then also automatically fetch the associated cryoEM map if there is one? Looking in the mmCif file, there is a flag for the associated emdb-map (e.g. in 5ljo the mmCIF file there is a _pdbx_database_related.db_id flag with the corresponding id. It would be useful if this could be added as a flag to the open command if it isn't already. I'm sure it is also possible in some kind of script but I'm not hugely familiar with how to script in chimeraX.

[Tom Goddard]

Done.

Example

open 7pkz fetchEmdbMap true

I added an option when opening an mmCIF file to fetch an EMDB map whose EMBD id is found in the mmCIF file in the pdbx_database_related or database_2 mmcif tables. If no EMDB map id is found then a warning is logged saying that no EMDB id was found in the mmcif file.