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
>
>
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