Dear Dr. Morsey,
Here are instructions on how to open AlphaFold3-generated structures in ChimeraX (I think this may have been the gist of your question?):
1. If you run a job on the AlphaFold server, you can download the results as a .zip file.
2. If you unzip it, you will see 15 files, 5 of which are .cif files.
There are 5 .cif files because for each job, AF3 produces five predicted structures by sampling the diffusion process five times.
The fold_(your job name)_model0.cif file is the one with the best metrics (ipTM, pTM)
3. You can open that .cif file in ChimeraX and work with it from there.
I hope this was useful. I will also point you to
our recent preprint here where we used AF3 to predict novel GLI-SUFU structures and ChimeraX to visualize/analyze them.
_________________________________
Lee Bardwell, Ph.D.
Professor and Vice-Chair,
Dept. of Developmental & Cell Biology
Dunlop School of Biological Sciences
University of California, Irvine
On Jan 22, 2026, at 8:36 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear
Ahmed Morsy,
That
is just showing the proteins as ribbons. Yes of course you can open protein structures and show them as ribbons. The labels of the protein names would need to be added separately, but you could do that with the 2D Labels tool or command.
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/2dlabels.html__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxakjtLEUcg$ >
See
general information: making images with ChimeraX
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/images.html__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxam_d4HduQ$ >
See
also example images and command scripts:
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/gallery.html__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxakKu_C4uQ$ >
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/features.html__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxal98FV43g$ >
I
hope this helps,
Elaine
-----
Elaine
C. Meng, Ph.D.
UCSF
Chimera(X) team
Resource
for Biocomputing, Visualization, and Informatics
Department
of Pharmaceutical Chemistry
University
of California, San Francisco
On Jan 22, 2026, at 3:10 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Elaine Meng,
Greetings, and Happy New Year.
I hope you are doing well. I am writing to ask for your kind advice regarding a recent and excellent paper entitled “Regenerative Hair Pigmentation via Skin Organoids: Adaptive Patterning Mediated by Collagen VI and Semaphorin 3C.”
In this study, the authors performed AlphaFold3-aided protein docking of SEMA3C with NRP1 and PLXNA4 and presented structural figures illustrating these interactions. I have attached the relevant figure ( at the end of this meesage) for your reference.
May I kindly ask whether it is possible to generate similar structural visualization figures using UCSF ChimeraX? If so, I would greatly appreciate your guidance on whether ChimeraX can directly handle AlphaFold3-predicted complexes and produce comparable representations.
Thank you very much for your time and kind consideration. I look forward to your advice.
With best regards,
=========================
Ahmed Morsy, Ph.D.
Assitant Professor,
Department of Stem Cell & Regenerative Biotechnology,
Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
C.P.: +82/10-5299-5844
E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr
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Scopus id: 55258308400 (https://urldefense.com/v3/__https://www.scopus.com/authid/detail.uri?authorId=55258308400__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxanvuJGEtw$ )
Researchgate: https://urldefense.com/v3/__https://www.researchgate.net/profile/Ahmed-Abdal-Dayem__;!!CzAuKJ42GuquVTTmVmPViYEvSg!NfysFzCkRqLHQvhkxbQTEiAOC-XbH8LB2wWp8qAiwMp1vdlyCDBK6Sk-zIq5RRMGYuSrBI8W0Y-RIs-yTrQAxammKWdVVw$
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