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, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 On Saturday, December 14, 2024 at 02:35:50 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, 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 _______________________________________________ ChimeraX-announce mailing list -- chimerax-announce@cgl.ucsf.edu To unsubscribe send an email to chimerax-announce-leave@cgl.ucsf.edu
