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. In my opinion the superposition by O seems much better, after looking at the structure. 

 

Apart from the difference in the RMSD, I would like to plot the RMSD values against the no. of ca atoms superposed. That i only know to do through superpose. Is there is any way to plot the RMSD values i get from O against the no. of ca atoms. I would appreciate the help. 

 

Thanks in advance.

peter