id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17918	Difference in secondary structure display between Mol* 3D and ChimeraX	paul.kirchberger@…	Eric Pettersen	"{{{
Hello,
upon importing an Alphafold3 prediction (which as far as I can tell used the PDB Mol*3D viewer to display results) into ChimeraX 1.1 and trying to draw a fold diagram based on it, I noticed that ChimeraX was missing and/or shortening the display of certain secondary structures. I have attached screenshots for Mol*3d and ChimeraX:

[cid:fd040d24-4c98-469e-8881-7da7c3a649b8]
[cid:5b8b968d-769e-4b61-96a3-c6c16f22a8f9]


As you can see the beta sheet starting at ALA67 (highlighted in both pictures) is much shorter in ChimeraX, and the beta sheet after the turn is missing altogether.

Saving the file from ChimeraX and re-uploading it to the PDB viewer gives the chimeraX result:
[cid:46d89741-fcf9-433b-8775-48b247f356f0]


I have attached the .cif file in question.

I have not tried to systematically figure out what causes this discrepancy, I have really only noticed it here, but it is very annoying when trying to draw fold diagrams. Any idea what is going on?

cheers

Dr. Paul Kirchberger
Assistant Professor
Department of Microbiology and Molecular Genetics
Oklahoma State University
Stillwater, OK 74078

[cid:image001.png@01D77897.E8EBA0B0]

}}}

[[Image(image.png)]]

[[Image(image-1.png)]]

[[Image(image-2.png)]]

[[Image(Outlook-cid_image0.png)]]

[attachment:""fold_err3063490_k141_167892_gp5_model_0.cif""]
"	defect	closed	normal		Structure Analysis		not a bug						all	ChimeraX