Subject: Request for Detailed Clarification on ChimeraX RMSD, Alignment Metrics, and Pruning Calculations
Hello, Good day. I am using ChimeraX for an academic research project involving protein structure comparison. Before proceeding with my analysis, I would like to request detailed clarification on how ChimeraX obtains specific structural comparison values. In particular, I would like to understand: how ChimeraX gets these values and what formulas or computational methods are used for each measurement. Specifically, I would like to ask about the following: 1. The recommended procedure for computing RMSD between two protein structures in ChimeraX, including the appropriate steps, commands, and settings to ensure a correct and reproducible measurement. 2. How ChimeraX determines aligned residue pairs during Matchmaker or similar alignment tools, including how residues are selected or excluded based on sequence alignment and structural fit. 3. The exact meaning and calculation method for “pruned atom pairs” in the alignment results. In particular, I would like clarification on the pruning process (for example, removal of atom pairs whose distances exceed a threshold) and how this affects the final reported values. 4. Whether RMSD in ChimeraX is calculated using all aligned atom pairs, pruned atom pairs only, or whether both values are available. I would also like to understand how to correctly interpret RMSD before pruning versus RMSD after pruning. 5. How ChimeraX performs structural alignment when the two sequences are identical but the predicted models have local deviations such as altered loops, turns, flexible regions, or insertions. 6. Recommended best practices when comparing three types of structures: • an experimental PDB crystal structure • an AlphaFold predicted structure • a Swiss-Model homology model 7. Any documentation, reference materials, or example workflows that explain the statistical reporting of structural comparison in ChimeraX, especially the following values: • RMSD, calculated as √(1/N Σ di²) • distance measurements between paired atoms, defined as √[(x1 − x2)² + (y1 − y2)² + (z1 − z2)²] • aligned residue counts • pruning thresholds and post-pruning atom pair counts This information will help ensure that the statistical evaluation in my study (including RMSD, aligned residues, and pruned atom pairs) is methodologically correct and consistent with ChimeraX standards. Thank you very much for your time and assistance. Your guidance will greatly improve the accuracy and reliability of my research analysis. Best regards, [Your Name] -- *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).*
Dear [Your Name], All of this information is in the Matchmaker manual page: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> If you run it with the same parameters on the same structures, you will get the same answer (reproducible). 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 5, 2025, at 5:06 AM, EMMANUEL JAIME SIBAYAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, Good day. I am using ChimeraX for an academic research project involving protein structure comparison. Before proceeding with my analysis, I would like to request detailed clarification on how ChimeraX obtains specific structural comparison values. In particular, I would like to understand: how ChimeraX gets these values and what formulas or computational methods are used for each measurement. Specifically, I would like to ask about the following: • The recommended procedure for computing RMSD between two protein structures in ChimeraX, including the appropriate steps, commands, and settings to ensure a correct and reproducible measurement. • How ChimeraX determines aligned residue pairs during Matchmaker or similar alignment tools, including how residues are selected or excluded based on sequence alignment and structural fit. • The exact meaning and calculation method for “pruned atom pairs” in the alignment results. In particular, I would like clarification on the pruning process (for example, removal of atom pairs whose distances exceed a threshold) and how this affects the final reported values. • Whether RMSD in ChimeraX is calculated using all aligned atom pairs, pruned atom pairs only, or whether both values are available. I would also like to understand how to correctly interpret RMSD before pruning versus RMSD after pruning. • How ChimeraX performs structural alignment when the two sequences are identical but the predicted models have local deviations such as altered loops, turns, flexible regions, or insertions. • Recommended best practices when comparing three types of structures: • an experimental PDB crystal structure • an AlphaFold predicted structure • a Swiss-Model homology model • Any documentation, reference materials, or example workflows that explain the statistical reporting of structural comparison in ChimeraX, especially the following values: • RMSD, calculated as √(1/N Σ di²) • distance measurements between paired atoms, defined as √[(x1 − x2)² + (y1 − y2)² + (z1 − z2)²] • aligned residue counts • pruning thresholds and post-pruning atom pair counts This information will help ensure that the statistical evaluation in my study (including RMSD, aligned residues, and pruned atom pairs) is methodologically correct and consistent with ChimeraX standards. Thank you very much for your time and assistance. Your guidance will greatly improve the accuracy and reliability of my research analysis. Best regards, [Your Name]
participants (2)
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Elaine Meng -
EMMANUEL JAIME SIBAYAN