Re: [IMP-dev] Residue number vs residue index

[Ben Webb <>]

On 5/3/11 3:23 PM, Daniel Russel wrote:
> It was pointed out that the thing we call a "residue index" in imp
> appears to be more commonly referred to as a "residue number" (that
> is, the number  of the residue as stored in the pdb file).

Whoever pointed that out was incorrect. ;) The two are subtly different:

- Residue index is sequential; you are (pretty much) guaranteed that
  residue(our index+1) is the next residue and residue(0) is the first
  residue in a chain.
- PDB residue number is not sequential, and in fact may not even be a
  number. ;) Since the residue number is derived from the sequencing,
  you may have gaps in the numbering (if structures are not available)
  which I guess is no big deal, or you may have extra residues with
  insertion codes (e.g. PDB residue numbers may go 4, 5, 6, 6A, 6B, 7,
  15, 16).

Before forcing the two to be the same you'll have to figure out what to 
do with insertion codes.

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle