Open tonyelewis opened 6 years ago
To be more precise... these all work under PDB_DSSP_SEC
, eg:
cath-ssap --prot-src-files PDB_DSSP_SEC 1dleB02 2hntE00
...but fail under PDB_DSSP
, eg:
cath-ssap --prot-src-files PDB_DSSP 1dleB02 2hntE00
I will change the title accordingly.
I've looked a little bit into 1dx5I02 versus 1yukB02 and found that:
PDB_DSSP_SEC
is that it's doing a fast_ssap; the following slow_ssap it does fails.PDB_DSSP
is because it doesn't do a fast_ssap because it deduces that there aren't any secondary structures in 1dx5I02prosec
has assigned five beta-strand secondary structures: residues with indices (offset 1) 5-8, 8-11, 17-20, 25-28, 30-33, which correspond to residues 394-397, 397-400, 406-409, 414-417, 419-422prosec
has assigned beta-strands to the middle two.So this could probably fixed by more work to improve the code's ability to replicate the behaviour in prosec
/ secmake
. That should be done with (a) test-cases to demonstrate the specific improvement (b) the use of large-scale comparisons to ensure that specific changes are reducing overall errors, not increasing them.
But it's also worth noting that all the versions are failing to achieve anything in the slow ssap here and that's probably the more significant problem.
Note that these don't work with
--prot-src-files
ofPDB_DSSP
either.Examples where both proteins have ≥ 30 residues :