[ccp4bb]: tricking TOPP

[diane h peapus <dp72@cornell.edu>]

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Hello All:

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....
almost....

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...

RESIDUE 1          
DISTANCE 10.0      

But it doesn't change the errors at all.

Are there any suggestions out there?

thanks
diane
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