[phenixbb] alternatives to RMSD

[MARTYN SYMMONS]

That's a reasonable approach and I think that it is similar to the one used by FATCAT - which I notice is the basis for structural comparison at the RCSB site. 
Motivation and some results in the paper ( http://www.ncbi.nlm.nih.gov/pubmed/14534198) 

It's not clear to me, though, how to fairly compare the resulting RMSD of fragments with twists between.  If I introduce an arbitrary number of twists then I can improve the rmsd artificially. In sequence matching there is a penalty for introducing a gap and that is scaled compared with the amino acid substitution scoring to split the match into a 'reasonable' number of sub-alignments. Obviously in 3D case there should also be a penalty for introducing a split in the structure to do a twist re-orientation - but how to quantify it compared with RMSD and get a global score?

Seems to me better would be to express the whole problem in torsional space - so the twists would be large displacements while the matched sections should have close fit in torsional angles. And a global score could be calculated. Someone must have tried this? 

All the best
Martyn 
Cambridge 
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