peter hudson wrote:
Hello all
I superposed the two different chain, which are two different subunits
of the same structure which are different in conformation with two
differen t programmes.
1) First is with O, with LSQ command, it gives the RMSD values for
different chain is 1.5A for 108 ca atoms.
2) Second programme i used is Superpose from CCP4i inbuilt, which gives
the RMSD values of 2.4A for almost same ca atoms.
Why this two programmes output RMSD are very different.
The devil's in the detail. If you were using ccp4i, which superpose
option did you use?
(If you used "superpose using secondary structure matching" then that is
very different to LSQ/LSQKAB matching - and you would expect a different
rmsd).
Paul.
