How to obtain transformation matrix between protein structures
Hi,
I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix.
With Regards,
Qiancheng Xia
National Institute of Biological Sciences
Beijing, China
2023/10/20
Hi Qiancheng Xia, Please use the chimerax-users@cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX.
Chimera does not have the reportMatrix option.
As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards,
Qiancheng Xia
National Institute of Biological Sciences
Beijing, China
2023/10/20
Hi Elaine, I've found a way to do that in Chimera. The command is below: """ matchmaker #0 #1 measure rotation #0 #1 """ Then a transformation matrix will be output in log. I've tested and it works.
By the way, the command I've used in ChimeraX is exactly "matchmaker #0 to #1 reportMatrix true". And that doesn't work. I've tested other keywords listed in documentation and they all work. My ChimeraX version is """ $ chimerax --version UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. """
With Regards,
Qiancheng Xia
Beijing, China
2023/10/21
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间:2023-10-21 00:05:38 (星期六) 收件人: 夏前程 xiaqiancheng@nibs.ac.cn 抄送: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu, "ChimeraX Users Help" chimerax-users@cgl.ucsf.edu 主题: Re: [Chimera-users] How to obtain transformation matrix between protein structures
Hi Qiancheng Xia, Please use the chimerax-users@cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX.
Chimera does not have the reportMatrix option.
As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards,
Qiancheng Xia
National Institute of Biological Sciences
Beijing, China
2023/10/20
Hi, You need to use the newer daily build, because the reportMatrix option was added after the release of ChimeraX 1.6.1. Also there is no #0 in ChimeraX, so it would be something like
matchmaker #2 to #1 reportMatrix true
If you use the Help menu it will match your installed version. Documentation on our website may be newer than the software version you have installed.
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2023, at 7:33 PM, 夏前程 xiaqiancheng@nibs.ac.cn wrote:
Hi Elaine, I've found a way to do that in Chimera. The command is below: """ matchmaker #0 #1 measure rotation #0 #1 """ Then a transformation matrix will be output in log. I've tested and it works.
By the way, the command I've used in ChimeraX is exactly "matchmaker #0 to #1 reportMatrix true". And that doesn't work. I've tested other keywords listed in documentation and they all work. My ChimeraX version is """ $ chimerax --version UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. """
With Regards,
Qiancheng Xia
Beijing, China
2023/10/21
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间:2023-10-21 00:05:38 (星期六) 收件人: 夏前程 xiaqiancheng@nibs.ac.cn 抄送: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu, "ChimeraX Users Help" chimerax-users@cgl.ucsf.edu 主题: Re: [Chimera-users] How to obtain transformation matrix between protein structures
Hi Qiancheng Xia, Please use the chimerax-users@cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX.
Chimera does not have the reportMatrix option.
As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards,
Qiancheng Xia
National Institute of Biological Sciences
Beijing, China
2023/10/20
participants (2)
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Elaine Meng -
夏前程