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[ccp4bb]: tricking TOPP
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I'm trying to calculate rmsd's for loops of interest in different
proteins and have tried a few different methods. I found that...
1) CNS calculated rmsd for each residue, but both structures have
to be described by the same .mtf file, so I can't evaluate same
protein from different species easily.
2) DALI gives a single overal rmsd for the whole protein, but I
am interested in certain loops.
3) TOPP breaks the rmsd's down into 2nd structure, calculating
rmsd's for each alpha-helix and beta-strand, but not for loops.
So, I did what I think has tricked TOPP into doing what I want....
I made an artificial set of HELIX cards listing all my loop
residues as helices. This way, I bypass TOPP's eveluation
of secondary structure and it just does the rmsd's on what
I've already 'evelauted' as helices. Problem is when a loop
contains only 2 residues or when the rms is larger than 2.0.
In those cases, the rms is not calculated for that section
and I get errors that look like this....
helix: 11 have rms 4.117280 rejected
helix 12 not more than 2 atoms, rejected
Helix 13 rms is 2.6 more than 2.0 rejected
I've tried changing these...
But it doesn't change the errors at all.
Are there any suggestions out there?
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