Hi Vinita, Whenever you don't see some tool or command that was explained to you, it is probably because you need to get a newer version of ChimeraX. You should just try that first. According to Change Log, the "Minimize Structure" tool and "minimize" command were added in October and are in the 1.11 release and newer. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> You can "mutate" amino acids with swapaa command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html> - or - the Rotamers tool <https://rbvi.ucsf.edu/chimerax/docs/user/tools/rotamers.html> ... or another approach is to just predict the structure of the whole sequence, such as by using Modeller Comparative for homology modeling, or by machine learning approaches AlphaFold, or Boltz, or ESMFold. There are help pages for each of these tools, see the Tools index: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#tools> 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 Dec 22, 2025, at 4:05 AM, Vinita Pant via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Also, I need to modify a few amino acids in the PDB sequence to align with the UniProt sequence. Could you provide guidance on how to effectively make these changes? I’ve reviewed the instructions in the help window, but I wasn't able to implement them successfully. Thank you for your assistance.
Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943
On Mon, 22 Dec 2025 at 13:24, Vinita Pant <vinipant78@gmail.com> wrote: Thank you for your prompt response. With your help, I successfully prepared the file. However, I'm currently facing another challenge with the the 'energy minimization' step. I am unable to locate the energy minimization tool in the structure editing, as shown in the link you shared, in my version of ChimeraX. I’ve attached an image for clarity. Could you please guide me on how to perform energy minimization?
Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943
On Fri, 19 Dec 2025 at 22:15, Elaine Meng <meng@cgl.ucsf.edu> wrote: HI Vinita, I changed the email subject line to something descriptive.
Adding missing amino acid sidechain atoms can be done with the Dock Prep tool, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/dockprep.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 Dec 19, 2025, at 5:40 AM, Vinita Pant via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team, I am currently using ChimeraX 1.10.1 (2025-07-24) for preparing my protein for molecular docking, and I would like your guidance on repairing missing side chain atoms. I have explored several resources but have not yet found a solution. I appreciate any assistance you can provide to help me navigate this process effectively. Thank you for your support.
Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943
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