Re: [chimerax-users] Help getting rmsd value per residue of 2 similar structures.
Hi Binh, This is almost the same question as asked yesterday on chimerax-users@cgl.ucsf.edu, so I have the same answer:
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html
That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html
Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX.
Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users@cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 12:39 PM, Binh Nguyen AnBinh.Nguyen@UTSouthwestern.edu wrote:
Dear Elaine,
Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD.
I have found this too but I have no idea how to get such information. https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html
Please help, thank you.
B
Got it. Thank you very much.
B
_____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases
Peter O’Donnell Jr. Brain Institute
UT Southwestern Medical Center
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, February 8, 2023 2:56 PM To: Binh Nguyen AnBinh.Nguyen@UTSouthwestern.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: Help getting rmsd value per residue of 2 similar structures.
EXTERNAL MAIL
Hi Binh, This is almost the same question as asked yesterday on chimerax-users@cgl.ucsf.edu, so I have the same answer:
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html
That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html
Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX.
Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users@cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 12:39 PM, Binh Nguyen AnBinh.Nguyen@UTSouthwestern.edu wrote:
Dear Elaine,
Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD.
I have found this too but I have no idea how to get such information. https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html
Please help, thank you.
B
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