How to save coordinates of a fit atomic model
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
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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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 Laboratoire/laboratory: Marion 214C Tél./Phone: (613) 562-5800 #3976 fcampbel@uottawa.ca<mailto:fcampbel@uottawa.ca> https://fxcampbellvalois.org<https://fxcampbellvalois.org/> https://www.researchgate.net/profile/Francois_Xavier_Campbell-Valois https://ca.linkedin.com/in/fxcampbellvaloishostpathogen -- 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<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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Cfcampbel%40uottawa.mail.onmicrosoft.com%7Cfe2e8ae008194b84b12f08ddb29de28d%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638863113414770023%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5Vu1o1GPxVWRqXAQhmPxOqFki6aKn5EsMwTJTAby4Z8%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
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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
Laboratoire/laboratory: Marion 214C Tél./Phone: (613) 562-5800 #3976
fcampbel@uottawa.ca <mailto:fcampbel@uottawa.ca> https://fxcampbellvalois.org <https://fxcampbellvalois.org/> https://www.researchgate.net/profile/Francois_Xavier_Campbell-Valois https://ca.linkedin.com/in/fxcampbellvaloishostpathogen --
From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Monday, June 23, 2025 at 5:35 PM To: horvath.peter.3@pte.hu <mailto:horvath.peter.3@pte.hu> <horvath.peter.3@pte.hu <mailto:horvath.peter.3@pte.hu>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto: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.... <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 <mailto: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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.u... <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.u... <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Elaine Meng -
Eric Pettersen -
Francois-Xavier Campbell-Valois -
Tom Goddard