Get bond angles for nucleotides in pdb/cif structure file

Question

[noodle]

Hi Biostars,

Is someone aware of a tool that can return the bond angles across all nucleotides in a chain from a PDB file? I'm particularly interested in nucleotides from ribosome structures. Thanks!

Answer 1

[dthorbur]

MDanalysis is a python package that should be able to do this for you. The MDAnalysis.analysis.bat function calculates bond length, angle, and torsion for bonded atoms.

In the readme, they have an example of how to do this across atom groups, which you can probably use apply as nucleotides (though, I've not used this function myself).