The "save" command also has the "relModel" option for specifying saving relative to another model. E.g. if you fit the atomic model #2 to the map model #3, you may want to save the atomic model relative to the map: save blahblah.cif model #2 relModel #3 See the "save" mmCIF help for the relevant command options for mmCIF: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif> I hope this helps, Elaine
On Jun 23, 2025, at 2:19 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Peter,
To save an atomic model after you have moved it to fit into a map use menu File / Save..., file type mmCIF, uncheck "Use untransformed coordinates", and save. If you have multiple models open it won't show that option and instead will show "Save relative to model: <menu>" and choose to save relative to the map.
Or if you want to use a command just use "save myfitmodel.cif". If you have multiple models open you have to specify in the command which to save "save myfitmodel.cif model #3".
Please ask questions about how to use ChimeraX on the mailing list and not in bug reports. That way others can benefit from the answers.
Tom
Hi Tom, I’m having an issue in ChimeraX and would appreciate your help. I aligned an atomic model with a cryo-EM map and would like to save the atomic model in its aligned position, so that when I reopen both the map and the model later, they appear properly aligned. I tried using the GUI to save the transformed atomic model in different formats, but when I reopened the files, the alignment was lost. I also tried using the save command, but encountered the same issue — the model was saved in its original, unaligned coordinates. Finally, I attempted to save the session as a .cxs file and open it in Chimera, but Chimera cannot open .cxs session files from ChimeraX. Could you please tell me exactly what I need to do to save the atomic model with its current (transformed) coordinates so that it stays aligned with the map when reloaded? Thank you very much for your help. Wishing you a great day, Peter
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