how MatchMaker computes RMSD and alignment scores
Dear ChimeraX Team, Dear ChimeraX Team, Thank you for the documentation on the MatchMaker tool. It explains well how the tool works. I would like to ask a very simple clarification for my thesis: How are the numerical values reported by MatchMaker actually calculated? Specifically: 1. What is the mathematical formula used to compute RMSD, and which atoms are used by default? 2. How does MatchMaker convert protein sequences into numerical alignment scores? 3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized? I just want to clearly explain how these numbers are obtained. Thank you very much. Best regards, Emmanuel Jaime S. Sibayan -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*
All of these are covered in the documentation (UCSF ChimeraX help pages) and paper cited therein, with the possible exception of RMSD, as the name itself root-mean-square displacement or distance, which is exactly how it is calculated. It is such a standard measure that it is unlikely you'd need to explain it in your thesis. You can web-search "RMSD" if you really need to show some equation. Which atoms are used by matchmaker are covered in the documentation. Help pages: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> Regards, 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 6:48 AM, EMMANUEL JAIME SIBAYAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
Dear ChimeraX Team,
Thank you for the documentation on the MatchMaker tool. It explains well how the tool works.
I would like to ask a very simple clarification for my thesis:
How are the numerical values reported by MatchMaker actually calculated?
Specifically:
1. What is the mathematical formula used to compute RMSD, and which atoms are used by default?
2. How does MatchMaker convert protein sequences into numerical alignment scores?
3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized?
I just want to clearly explain how these numbers are obtained.
Thank you very much.
Best regards, Emmanuel Jaime S. Sibayan
Thank you very much for the clarification. On Tue, Dec 23, 2025 at 12:54 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
All of these are covered in the documentation (UCSF ChimeraX help pages) and paper cited therein, with the possible exception of RMSD, as the name itself root-mean-square displacement or distance, which is exactly how it is calculated. It is such a standard measure that it is unlikely you'd need to explain it in your thesis. You can web-search "RMSD" if you really need to show some equation. Which atoms are used by matchmaker are covered in the documentation.
Help pages: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
Regards, 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 6:48 AM, EMMANUEL JAIME SIBAYAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team,
Dear ChimeraX Team,
Thank you for the documentation on the MatchMaker tool. It explains well how the tool works.
I would like to ask a very simple clarification for my thesis:
How are the numerical values reported by MatchMaker actually calculated?
Specifically:
1. What is the mathematical formula used to compute RMSD, and which atoms are used by default?
2. How does MatchMaker convert protein sequences into numerical alignment scores?
3. Is the alignment score simply a sum of substitution matrix values, secondary-structure scores, and gap penalties, or is it weighted or normalized?
I just want to clearly explain how these numbers are obtained.
Thank you very much.
Best regards, Emmanuel Jaime S. Sibayan
-- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*
participants (2)
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Elaine Meng -
EMMANUEL JAIME SIBAYAN