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
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