Alpha-fold-chimerax-coot - incompatibility
Hi All, I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ? Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference. Thank you. [cid:d13d01b7-12bf-4117-8bbe-f63d6679629a@namprd08.prod.outlook.com]
Your .cif file likely has invalid data. For instance there are author assigned and reference chain ids in mmcif and perhaps one of those variants is mangled in what Coot wrote. We will not be able to help unless you provide the file. Tom
On Dec 1, 2025, at 12:59 PM, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All,
I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ?
Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference.
Thank you.
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Ideally, you would use ChimeraX's Help / Report a Bug to report this and include the problematic .cif file. If you need to keep the file private, you can send it to me directly. With the bug report, I'd be able to reproduce the problem you're having, and I'd be able to tell you if a recent version of ChimeraX has fixed the problem, or when the problem is fixed. You should also look at the warnings given in the log when you try to open the .cif file. Many modelling programs output incomplete/bad .cif files and those warnings should give you a clue about what's wrong. I am very interested in getting examples of mmCIF files that are problematic for ChimeraX. -- Greg On 12/1/2025 12:59 PM, Abhilash Padavannil via ChimeraX-users wrote:
Hi All,
I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ?
Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference.
Thank you.
participants (3)
-
Abhilash Padavannil -
Greg Couch -
Tom Goddard