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