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