Hello! I've been trying to use "sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original" to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try? Thank you, Alex
Hi Alex, That is extremely convoluted, but my guess is that want to use "name frozen" instead of just "name" -- If you simply use "name target sel" it will just sub in the word "sel" for "target" even if there are totally different atoms selected (or no atoms at all) at the time. So you gave two names to the same thing (sel) and your final command was really rmsd sel to sel which of course specifies two identical sets of atoms which would of course be zero. See explanation of "name" vs. "name frozen" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> 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 1, 2024, at 10:06 AM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello!
I've been trying to use
"sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original"
to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try?
Thank you, Alex
_______________________________________________ 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/
Thanks, Elaine! It worked XD ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, November 1, 2024 2:39 PM To: Alexander Lee <Alex.H.Lee@outlook.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Using name of selection with rmsd command Hi Alex, That is extremely convoluted, but my guess is that want to use "name frozen" instead of just "name" -- If you simply use "name target sel" it will just sub in the word "sel" for "target" even if there are totally different atoms selected (or no atoms at all) at the time. So you gave two names to the same thing (sel) and your final command was really rmsd sel to sel which of course specifies two identical sets of atoms which would of course be zero. See explanation of "name" vs. "name frozen" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> 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 1, 2024, at 10:06 AM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello!
I've been trying to use
"sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original"
to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try?
Thank you, Alex
_______________________________________________ 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/
participants (2)
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Alexander Lee -
Elaine Meng