Different dihedral angle results between Chimera and ChimeraX
Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex
Alex, The angle command with four atoms will print the angle between the vector from atom 1 to atom 2 and the vector from atom 3 to atom 4. In your case it looks like this would be the bond between the methyl C and carbonyl C, and the nitrogen to the ring C. By eye, these bonds appear to be nearly parallel, so 7 degrees sounds reasonable. I'm not familiar with this convention for defining an angle with four atoms, but I see how it might be useful. But you're looking for the dihedral angle instead, which is what Chimera is printing. For dihedral/torsional angles, ChimeraX has the torsion command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/torsion.html Best, Tony On Thu, Jan 16, 2025 at 3:49 PM Alexander Hung Lee via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected
I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file.
Regards, 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/
Thank you! Alex Lee Woods Lab ahl63010@uga.edu ________________________________ From: Tony Schaefer <tony.schaefer.chem@gmail.com> Sent: Thursday, January 16, 2025 6:18 PM To: Alexander Hung Lee <Alexander.Lee@uga.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Different dihedral angle results between Chimera and ChimeraX You don't often get email from tony.schaefer.chem@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Alex, The angle command with four atoms will print the angle between the vector from atom 1 to atom 2 and the vector from atom 3 to atom 4. In your case it looks like this would be the bond between the methyl C and carbonyl C, and the nitrogen to the ring C. By eye, these bonds appear to be nearly parallel, so 7 degrees sounds reasonable. I'm not familiar with this convention for defining an angle with four atoms, but I see how it might be useful. But you're looking for the dihedral angle instead, which is what Chimera is printing. For dihedral/torsional angles, ChimeraX has the torsion command: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/torsion.html Best, Tony On Thu, Jan 16, 2025 at 3:49 PM Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:ii_194715da64ccb971f161] Regards, Alex _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto: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 Hung Lee -
Tony Schaefer