RMSD between nonidentical atomic models
Hi, If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case. I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
HI Roden, The "rmsd" command works fine -- you just have to specify in the command which atoms to use instead of the whole models, for example: rmsd #2:10-500@ca to #3:10-500@ca ... or maybe their residue numbers are different too, e.g. rmsd #2:14-353@n,ca,c,o to #3:12-351@n,ca,c,o See help on rmsd <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> See help on command-line specification of atoms, residues, chains, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> The main thing is that you have to figure which atoms go with which atoms yourself, instead of like matchmaker where it figures it out for you. Also matchmaker only uses CA atoms for the reported RMSD, so maybe you want to use more atoms. 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 Nov 24, 2024, at 11:23 PM, Roden Deng Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case.
I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models.
Thanks, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.<rmsd between nonidentical structures.jpg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
I see. Many thanks, Elaine! Best, Roden On Mon, Nov 25, 2024 at 7:54 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
HI Roden, The "rmsd" command works fine -- you just have to specify in the command which atoms to use instead of the whole models, for example:
rmsd #2:10-500@ca to #3:10-500@ca
... or maybe their residue numbers are different too, e.g.
rmsd #2:14-353@n,ca,c,o to #3:12-351@n,ca,c,o
See help on rmsd < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
See help on command-line specification of atoms, residues, chains, etc. < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
The main thing is that you have to figure which atoms go with which atoms yourself, instead of like matchmaker where it figures it out for you. Also matchmaker only uses CA atoms for the reported RMSD, so maybe you want to use more atoms.
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 Nov 24, 2024, at 11:23 PM, Roden Deng Luo via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://urldefense.com/v3/__https://alphafold.ebi.ac.uk/files/AF-P32565-F1-m... to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case.
I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models.
Thanks, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.<rmsd between nonidentical structures.jpg>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
participants (2)
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Elaine Meng -
Roden Deng Luo