Hello,
I'm using Jmol 14.13, which should use the DSSP v2.0 algorithm to compute
secondary structure. The command $show defaultStructureDSSP returns true, so
this
should indeed be the case. However, Jmol displays residues 365-368 from
7odc.pdb as loop-type, not ribbon, while DSSP 2.0 computes this stretch as type
E, part of a strand that strectches from residue 365 to residue 373. To
complicate matters, at residue 369 Jmol does not not start the ribbon at the
residue's nitrogen but instead at its alpha carbon.
However, if I issue the command $calculate structure and then redisplay, the
structure is then shown with a ribbon consistent with DSSP, running from 365 to
373. Can anyone tell me why Jmol doesn't display this stretch according to DSSP
in the first place? It's true that a ramachandran angle calculation does show
the stretch 365 to 368 as loop-type with no ribbon, so perhaps for some reason
Jmol is doing a ramachandran calculation instead of DSSP for these residues,
but then still doesn't explain why the ribbon starts at residue 369's alpha
carbon instead of its nitrogen.
It's worth noting that this stretch is somewhat ambiguous in secondary
structure. Although it shows strand-like H-bonding with an adjacent strand, the
chain bends tightly enough at these residues to fit the definition of a beta
turn. Does Jmol override DSSP in such cases?
Any insight is appreciated.
Nicholas Newell
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