This is an alphanumeric field that identifies a PDB residue
within a chain. It looks exactly as if taken from (1-based)
columns 23 through 27 of the ATOM record of the PDB file. In
general, this will not be an integer, since there are sequence
numbers like " 235A". The first four characters
are digits, with blank padding on the left, and the fifth and
last character is either a letter suffix or blank. See the PDB sequence number
description for further caveats.
By prefixing the chain ID to a pdbres field, one can create a
pdb-index. [The code has recently
started evolving to use the more complete pdb-index fields
instead of pdbres fields, since one needs an explicit chain for
multichain cores. -- rgr, 27-Jul-98.]
segment type
Segment types are strings that convey the nature of the segment.
[Note: Elsewhere this is called the "segment designator"
or "segment descriptor"; the terminology should be standardized.
-- rgr, 21-Aug-96.] All helices are of type "H"; all
other segments are strands of various sorts. The labels fall
into three classes:
- Helices are uniformly denoted by "H".
- Open-sheet strands are denoted
"En", where n is the sheet number.
(Sheet numbers are assigned arbitrarily in order of the
first residue in the sheet.)
- Cyclical strands (i.e. strands comprising a barrel
structure) are denoted by "Cxxyyzz", where
xx is the number of this strand,
yy is the number of a neighboring strand,
and zz is the number of the other
neighboring strand (the choice of neighbors is arbitrary
at present). Numbers are assigned to strands according to
the order of their first residue, whether or not they
appear in a barrel.
Note that sheet indices and the strand indices used to name
barrel segments are numbered for the PDB entry as a whole, and
not chain by chain. This should work fine for most code, which
only cares whether strand residues are part of the same sheet or
not. (In principle, barrels are trickier, since one cannot
assume that a core model includes only one barrel; one must trace
the barrel around to find if two strands are on the same barrel.
In practice, 1tie seems to be the only model with more than one
barrel, and it appears to be pathological in any case. -- rgr,
21-Aug-96.)
[And many score functions care only whether a segment is a
helix or a strand. The code that generates these labels is also
under development; the assignment is not always unique, so our
heuristics may change. -- rgr, 31-Jul-96.]