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
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
participants (2)
-
Binh Nguyen -
Elaine Meng