Hi François,
The information about how to unsubscribe is at the bottom of every mail message from the list, including this one.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Jun 24, 2025, at 2:11 AM, Francois-Xavier Campbell-Valois via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Good Morning,
                               Can you please remove my email from this list or provide me with instructions to do so?
 
Thank you,
 
F-X
 
François-Xavier Campbell-Valois, PhD
Professeur agrégé/Associate Professor

Université d’Ottawa/University of Ottawa
Département de chimie et sciences biomoléculaires/
Department of Chemistry and Biomolecular Sciences
Pavillon D’Iorio| D’Iorio Hall
10 Marie-Curie Private
Ottawa ON
K1N 9A4
CANADA

Cross-appointed/Affectation secondaire:
Département de Biochimie, Microbiologie et Immunologie
 
Bureau/Office: DRO 403
-- 
 
 

From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Date: Monday, June 23, 2025 at 5:35 PM
To: horvath.peter.3@pte.hu <horvath.peter.3@pte.hu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Re: How to save coordinates of a fit atomic model

Attention : courriel externe | external email

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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fsave.html%23mmcif&data=05%7C02%7Cfcampbel%40uottawa.mail.onmicrosoft.com%7Cfe2e8ae008194b84b12f08ddb29de28d%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638863113414739154%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qdEwbZDGBIhH8ph670rrLNJ48CmeTsW3Si3oVnerL6c%3D&reserved=0>

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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