Just use dssp and cite it. For cartoon figures, if you provide a disclaimer, it doesn't hurt to tweak it a bit to make it look better.
The idea is that readers are supposed to know that a protein doesn't really look like a cartoon--and those who don't understand the distinction probably won't have enough knowledge to have an opinion about your assignments anyway. James On Apr 8, 2011, at 9:19 AM, Cale Dakwar wrote: > 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
