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://rbvi.ucsf.edu/chimerax/docs/user/tools/2dlabels.html> See general information: making images with ChimeraX <https://rbvi.ucsf.edu/chimerax/docs/user/images.html> See also example images and command scripts: <https://www.rbvi.ucsf.edu/chimerax/gallery.html> <https://www.rbvi.ucsf.edu/chimerax/features.html> 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 Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en <1769080147269blob.jpg>