Use minimization in chimerax using command line
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 _____________________________________________ Vineet Jain (Chancellor) Inspiration
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://www.rbvi.ucsf.edu/chimerax/progress.html> 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
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<https://aka.ms/AAb9ysg> ________________________________ 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<https://www.rbvi.ucsf.edu/chimerax/progress.html>> 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
I may not understand the question. The Dock Prep in ChimeraX works the same way as in Chimera so you might as well just use Chimera for the whole process. There are Chimera commands for dockprep and minimization. I cannot decide for you which command options you want, you will have to determine that yourself based on the details of your project. Also remember that minimization is only relaxation to a local minimization, and does not really predict global changes from a mutation (loss of stability or folding, or even any larger conformational changes). Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 29, 2025, at 10:23 AM, TUSHAR GUPTA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.u...>
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Okay I got your point. Thank you Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, May 29, 2025 11:01:13 PM To: TUSHAR GUPTA <E24SOEP0001@bennett.edu.in> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Use minimization in chimerax using command line I may not understand the question. The Dock Prep in ChimeraX works the same way as in Chimera so you might as well just use Chimera for the whole process. There are Chimera commands for dockprep and minimization. I cannot decide for you which command options you want, you will have to determine that yourself based on the details of your project. Also remember that minimization is only relaxation to a local minimization, and does not really predict global changes from a mutation (loss of stability or folding, or even any larger conformational changes). Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 29, 2025, at 10:23 AM, TUSHAR GUPTA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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.
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://ind01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7C%7Ca5dbbdfb74494046e26a08dd9ed6a388%7C2c5bdaf48ff24bd9bd547c50ab219590%7C0%7C0%7C638841366927279255%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=PCNtNuYDF2K2yYv4SmegrIHz%2FVZrdNlwUwSwH1mfpY0%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
“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
participants (2)
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Elaine Meng -
TUSHAR GUPTA