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
