Hi Sam, This is not opening both in a single command, but may still be a convenience. After opening the atomic structure, you can use the "log metadata" command to show in the Log a table of associated information, which for 5ljo includes a link to open the associated map: When you first open 5ljo, the Log would show a "more info..." link that you can click, which just issues the "log metadata" command for you. Either way of executing that command gets you the info and action links shown above. 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 Sep 24, 2025, at 2:45 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.
Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited
