Dear Dr. Meng, Thank you so much for your detailed response and for providing the helpful links. I understand that ChimeraX’s minimization features are still a work in progress, and I appreciate your clarification. I will explore the Dock Prep tool and the available minimization options in ChimeraX. Your guidance has been very valuable, and I truly appreciate your time and support. Best regards, Ahmed Morsy =========================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 Monday, September 9, 2024 at 01:34:31 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Ahmed Morsy, ChimeraX does have a Dock Prep tool, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/dockprep.html> ...but it does not have general minimization, sorry, that is still work in progress. See the short list of features not yet in ChimeraX: <https://www.rbvi.ucsf.edu/chimerax/progress.html> There are some features in ChimeraX that can do a little minimization but it is not as complete as in Chimera. See: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> There are dynamics in the ChimeraX ISOLDE plugin, but it may be for advanced users such as cryo-EM structural biologists. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> 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 Sep 6, 2024, at 8:01 PM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:
Dear Dr. Elaine,
Greetings!
I hope this message finds you well.
I would like to inquire if ChimeraX offers options for fixing PDB files, specifically for correcting hydrogen bonds and performing energy minimization, in preparation for docking studies.
I look forward to hearing from you and appreciate your guidance.
Best regards, Ahmed Morsy