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
|