Thank you so much for your quick response. 
I have understood that we can add hydrogen, charge and perform dockprep in ChimeraX as initial steps for minimization. May you suggest me that process that I may use to minimise my structure, as I am aiming to analyse and understand the difference between a control or reference structure from PDB and an insilico induced mutated structure. 

Sent from Outlook for Android
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Thursday, May 29, 2025 10:48:07 PM
To: TUSHAR GUPTA <E24SOEP0001@bennett.edu.in>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Use minimization in chimerax using command line
 
Hello Tushar,
For now you will still need to use Chimera for minimization.

We are working on adding that feature to ChimeraX, but it is complicated and not yet available, sorry.

ChimeraX vs Chimera missing features:
<https://ind01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fprogress.html&data=05%7C02%7C%7Cfbe3ae017ab24f14331508dd9ed4d101%7C2c5bdaf48ff24bd9bd547c50ab219590%7C0%7C0%7C638841359126472478%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ecEKuV3tqj%2FAwnK7ZYJQMKZpBbzAehRfYN1lgIv19Uw%3D&reserved=0>

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 29, 2025, at 12:05 AM, TUSHAR GUPTA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Good morning
> I would like to appreciate your work and efforts in developing and maintaining ChimeraX, it has always been so useful tool in my research. I was initially using Chimera that had excellent feature of using amber force field for energy minimization of structure and making movie using topology and coordinate file.
> I am working on inducing mutation in nucleic acid and protein structures. I wish to incorporate the minimization step in my research using Chimerax.
> I will be highly grateful if you could guide me how can I use minimization steps in Chimerax using command line codes.
>
> Thank you
> Tushar Gupta
> PhD biotechnology
> Bennett University
> Greater Noida
> India
> “He that can have patience can have what he will.” – Benjamin Franklin
“He that can have patience can have what he will.” – Benjamin Franklin

_____________________________________________

Vineet Jain (Chancellor) Inspiration

“He that can have patience can have what he will.” – Benjamin Franklin

_____________________________________________

Vineet Jain (Chancellor) Inspiration