 |
 |
Are the chains numbered differently? the SUPERPOSE LSQ program requires you to specify which residues to superpose. And any RMS is wildly distorted by a few outliers.. Look at the list of > average differences to see if you have such a problem. The SSM superposition excludes outliers automatically. Eleanor Pavel Afonine wrote: > Hi Peter, > > you can also try superposition option in phenix: > > phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file] > > where optionally you can provide atom selections for "fixed" and > "moving". > > Pavel. > > > On 7/5/09 12:33 AM, 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. 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 > >