Well - the idea of NCS refinement is to restrain the 2 NCS related
models to be the same so that is problematic if they should be somewhat
diffeent..
You can get the matrix using SSM superposition ( see the GUi -
superpose molecules)
This will match using Secondary structure and give a list of what
matches what in the two chains.
You could then set up the restraints carefulyy
eg Chain A res 4 14 res 19 to 35 res 39 to xxx etc matching Chain B
res 2 to 12 20 36 41 to etc
You would presumably restrain maybe the main chain but not the side chains
However I am not sure how valuable it would be.
Eleanor
Radisky, Evette S. Ph.D. wrote:
>
> I have some questions about the "NCS Phased Refinement" task run from
> ccp4i:
>
> Can one use this task if there are multiple nonidentical chains in the
> NCS unit (e.g. a heterodimer), and if so, how does one define the NCS
> units? I find that the default is to consider each chain as a
> separate "NCS unit", and the program LSQKAB fails when trying to match
> residues between non-identical chains.
>
> Thanks,
> Evette
>
> Evette S. Radisky, Ph.D.
> Assistant Professor and Associate Consultant II
> Mayo Clinic Cancer Center
> Griffin Cancer Research Building, Rm 310
> 4500 San Pablo Road
> Jacksonville, FL 32224
> (904) 953-6372 (office)
> (904) 953-2857 (lab)
>
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