Hi,
I need to assign atom types for glycans and organic molecules. I can't
relly on the atom types in the pdb, since in general there is not atom type
information (e.g. all carbons are equal).
Does PyMOL offers some feature to make this assignment easier? like
checking the hybridization and valence of some given atom?
Is that's not the case I think one option could be to check the neighbors
for each atom. For some atom types It will be enough to check the first
neighbors (for example a CH3) but for other atom types I should check more
distant neighbors (eg to classify the "N of and amide" and the "N of
secondary amine")
Cheers,
Osvaldo.
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