[Jmol-users] question about mmCIF/PDB and secondary structure order

[Bob H. <ha...@st...>]

Here's a curious (common?) find relating to the differences between
mmCIF and PDB files. In this case, we are working with 1pgb.

(1) Notice carefully the ORDER with which the elements of structure
are read, and how that is different between the PDB file and the mmCIF file:


FileManager.openFile(1pgb.cif)
SmarterJmolAdapter:The Resolver thinks:Cif

SmarterJmolAdapter:Done reading... Found these strands:
SmarterJmolAdapter:Strand A, authorID=A, isBlank=true
SmarterJmolAdapter:Strand B, authorID=null, isBlank=false

(This sets strand A to be "0", by the way, but that's not my point.)

             res/chain res/chain

addstructure:   36 0   23 0 helix
addstructure:   12 0    9 0 turn
addstructure:   50 0   47 0 turn
addstructure:   20 0   12 0 sheet
addstructure:    9 0    1 0 sheet
addstructure:   56 0   50 0 sheet
addstructure:   46 0   42 0 sheet

--helix, then turn, then sheet

FileManager.openFile(1pgb.pdb)
SmarterJmolAdapter:The Resolver thinks:Pdb

             res/chain res/chain

addstructure:   36     23   helix
addstructure:   20     12   sheet
addstructure:    9      1   sheet
addstructure:   56     50   sheet
addstructure:   46     42   sheet
addstructure:   12      9   turn
addstructure:   50     47   turn

--helix, then sheet, then turn

(2) This presents an interesting question: What to do about
residues 50 and 9? Are they sheet or turn?

Is this common? Should "sheet" override "turn"? The other way around?

Curious,

-Bob