Sorry, I was unclear in my description of the problem.  I have NCS with 4 heterodimers in the ASU, and a good molecular replacement solution.  So I have 8 chains total -- A, B, C, and D are identical, and E, F, G, and H are identical to each other, but completely different from A, B, C, and D.  I want to use the "NCS Phased Refinement" task to generate averaged maps, improve phases with density modification, and to restrain refinement so that A, B, C, and D are restrained to match each other, and E, F, G, and H are restrained to match each other.  In the refmac5 task window, I can see how to set up NCS restraints this way, but in the "NCS phased refinement" task window, I don't see an equivlent way to define my restraints.  In this window, all I can do is make each chain an "NCS unit", and the task fails trying to compare A to E (which I don't really want it to do).

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)



-----Original Message-----
From: Eleanor Dodson [mailto:[log in to unmask]]
Sent: Thu 2/22/2007 3:42 AM
To: Radisky, Evette S.   Ph.D.
Cc: [log in to unmask]
Subject: Re: [ccp4bb] NCS Phased Refinement

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)
>