It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the same RESIDUE ID and give the RMSD
distance
There is documentation for it.
Eleanor
Jenny wrote:
Hi, All,
I have a question about rmsd calculation.
I have some pdbs (100 residues ) and these pdbs differ pretty much
only the loop region 40-60. Is there any easy way that I can
superimpose the fixed region ( 1-40,60-100) and then calculate the
rmsd for the loop?I need to calculate for each pair, so if there is
any script or program available to do this quickly, that would be great.
Thanks.
Jenny
