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
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
Of peter
hudson
Sent: Sunday, July 05, 2009 2:33 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] RMSD value is different from O and superpose
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
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
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
