mkdssp calculates spurious phi/psi angles between residues straddling discarded residue #86
Description
Consider this example (adapted from residues 217, 218 and 219 of chain A of PDB 3r8d):
ATOM 1 N GLY A 1 -21.821 -6.460 -44.110 1.00 44.43 N
ATOM 2 CA GLY A 1 -21.457 -5.215 -44.720 1.00 45.72 C
ATOM 3 C GLY A 1 -22.653 -4.708 -45.462 1.00 48.29 C
ATOM 4 O GLY A 1 -23.453 -5.519 -45.862 1.00 48.18 O
ATOM 5 CA GLU A 2 -23.199 -2.283 -45.588 1.00 73.09 C
ATOM 6 C GLU A 2 -23.609 -2.790 -46.930 1.00 69.74 C
ATOM 7 O GLU A 2 -24.724 -2.577 -47.369 1.00 69.31 O
ATOM 8 N ASP A 3 -22.684 -3.493 -47.558 1.00 69.04 N
ATOM 9 CA ASP A 3 -22.757 -3.856 -48.957 1.00 68.20 C
ATOM 10 C ASP A 3 -23.396 -5.203 -49.237 1.00 66.39 C
ATOM 11 O ASP A 3 -23.803 -5.469 -50.343 1.00 66.88 O
TER 12 ASP A 3
END
The mkdssp output, stripped of headers and intermediate columns, looks like this:
# RESIDUE AA [... ...] PHI PSI X-CA Y-CA Z-CA CHAIN
1 1 A G [... ...] 360.0-144.6 -21.5 -5.2 -44.7
2 3 A D [... ...] 24.3 360.0 -22.8 -3.9 -49.0
From what I understand... mkdssp has reasonably discarded residue 2 for not having an N atom record. But then since the C atom of 1 happens to be close enough to the N atom of 3, the check here hasn't put a break between 1 and 3. As a result, it has later calculated and printed phi/psi angles between 1 and 3, which are spurious and possibly misleading values because we know the input data has a different residue in between them.
I think it would be better if the code for ignoring residues (here) were able to explicitly insert a chain break (if there isn't already one there). What do you think?