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 
Inline image
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





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