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UCLOrengoGroup / cath-tools

Protein structure comparison tools such as SSAP and SNAP
http://cath-tools.readthedocs.io
GNU General Public License v3.0
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Unexpected superposition #34

Closed nataliedawson closed 7 years ago

nataliedawson commented 7 years ago

When running:

$ SSAP $1 $2 $ cath-superpose --ssap-aln-infile="$1$2.list" --pdb-infile="$DOMDIR/$1" --pdb-infile="$DOMDIR/$2" --sup-to-pymol-file="$1_$2.pml" $ pymol $1_$2.pml

where $DOMDIR=/cath/data/current/pdb, $1=2lf0A01 and $2=1lrzA03

The structural comparison with SSAP reported: a good SSAP score (78.25), good SSAP overlap (88%), and a poor RMSD (8.73A).

The issue:

Upon loading the .pml file with pymol, the two domains are superposed at a strange angle and show very little overlap, despite the very good overlap value calculated.

(Please note that I've added a .pdb.txt suffix to the domain PDB files as it would not support the filetype of the original file)

1lrzA03.pdb.txt 2lf0A01.pdb.txt

tonyelewis commented 7 years ago

The short version: use cath-ssap instead of SSAP and everything's OK:

sup

It turns out that the problem is basically that the alignment generated by SSAP is a bit dodgy and that's what causes the not-very-good superposition. cath-ssap does a better job.

tonyelewis commented 7 years ago

(...but this took me quite a while to figure out and triggered me to make some really useful improvements so it was a really worthwhile issue - thanks!)