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 automatic
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
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 dif
.ac.uk] On Behalf 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 c
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 program