Hello all, Given a PDB file of a newly solved protein structure, what is the standard procedure for assigning regions of secondary structure? And by this I mean to ask, how does one decide which residues form beta strands, which alpha helices, and so on? Is DSSP sufficient for this? Are we supposed to manually walk through the entire molecule and assign secondary structure as we deem appropriate based on hydrogen bonding behaviour? Some other procedure? And what of structures solved to ~2.7 A (or worse) where we can't be sure of H-bonding.
Cheers, Cale
