Dear Developers/Researchers of ChimeraX, I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script? Best, Zimiao
Dear Zimaio, You can see the per-residue "RMSD" by showing a sequence alignment with the structures associated and then displaying the RMSD header above the sequences. The sequence alignment can have 2 or more sequences, and the structures can be positioned using any method (not necessarily Matchmaker). You can also color one or more of the structures to show these RMSD values with the Render by Attribute tool. If you are using Matchmaker the superposition is only pairwise (2 sequences and 2 structures). Even if you superimpose >2 structures they are all pairwise to the specified reference structure. Matchmaker has an option to show the sequence alignment but you will get a separate sequence alignment for each pair. So in the simple case of only 2 structures, here is an example: open 2gbp open 2fw0 matchmaker #2 to #1 show true .... this automatically shows the sequence alignment with the RMSD header. The default is CA RMSD (alpha-carbons only) so in the case of only two structures, this is simply the CA-CA distance. You can use the Sequence Viewer context menu to show its Settings, Headers section if you want to change to backbone RMSD instead of CA RMSD. Context menu is shown with right-click on the tool (or ctrl-click if Mac). See Sequence Viewer help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> Then these RMSD values are automatically associated with the structure residues and can be saved to a file, or used for coloring, worm display, etc. as explained here. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> There is even a video on this process: <https://www.youtube.com/watch?v=XaTpB-UIxnU> I hope this helps, 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 Aug 5, 2024, at 10:35 AM, Zimiao Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Developers/Researchers of ChimeraX,
I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script?
Best,
Zimiao
Dear Elaine, Thank you so much for the timely response and helpful information! I was able to get the data required for calculations! Best, Zimiao ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, August 5, 2024 3:11 PM To: Zimiao Meng <zimiao.meng@duke.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Question regarding per-Residue RMSD Dear Zimaio, You can see the per-residue "RMSD" by showing a sequence alignment with the structures associated and then displaying the RMSD header above the sequences. The sequence alignment can have 2 or more sequences, and the structures can be positioned using any method (not necessarily Matchmaker). You can also color one or more of the structures to show these RMSD values with the Render by Attribute tool. If you are using Matchmaker the superposition is only pairwise (2 sequences and 2 structures). Even if you superimpose >2 structures they are all pairwise to the specified reference structure. Matchmaker has an option to show the sequence alignment but you will get a separate sequence alignment for each pair. So in the simple case of only 2 structures, here is an example: open 2gbp open 2fw0 matchmaker #2 to #1 show true .... this automatically shows the sequence alignment with the RMSD header. The default is CA RMSD (alpha-carbons only) so in the case of only two structures, this is simply the CA-CA distance. You can use the Sequence Viewer context menu to show its Settings, Headers section if you want to change to backbone RMSD instead of CA RMSD. Context menu is shown with right-click on the tool (or ctrl-click if Mac). See Sequence Viewer help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/s... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/s... > Then these RMSD values are automatically associated with the structure residues and can be saved to a file, or used for coloring, worm display, etc. as explained here. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/s... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/attribu... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/r... > There is even a video on this process: <https://urldefense.com/v3/__https://www.youtube.com/watch?v=XaTpB-UIxnU__;!!... > I hope this helps, 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 Aug 5, 2024, at 10:35 AM, Zimiao Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Developers/Researchers of ChimeraX,
I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script?
Best,
Zimiao
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Elaine Meng -
Zimiao Meng