Dear Dr. Elaine, Thanks for your detailed reply.It's helpful. Have a nice weekend! Best regards,Ahmed ========================= Ahmed Morsy, Ph.D. 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 Friday, October 11, 2024 at 12:24:22 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Ahmed, ChimeraX does not calculate TM-Score. You can calculate RMSD, but of course it depends on how the structures are superimposed. The Matchmaker tool and command will do the superposition and also report an RMSD, but the fitting and RMSD only use the CA atoms that were paired by sequence alignment. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> If you need to use more atoms for superposition, see the "align" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> If the structures are already superimposed, you can calculate RMSD over specified atoms using the "rmsd" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.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 Oct 10, 2024, at 4:46 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Elaine Meng,
I hope this message finds you well.
I would like to inquire if it is possible to calculate the RMSD value and TM-Score in ChimeraX to compare the differences between an experimental structure and an AlphaFold-predicted structure.
I look forward to your response.
Best regards, Ahmed