Hi Evette,
I believe that multi-chain NCS is what you'd like to use: something
like heterodimer AE NCS-restrained to BF, CG, DH.
You can do that using refmac5 ver 5.3.0015 and later version
If you go to
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
under the NCS section there is an explanation on how to set up this
kind of restrain.
Hope it helps,
Roberto
On 22 Feb 2007, at 11:28, Radisky, Evette S. Ph.D. wrote:
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:[EMAIL PROTECTED]
Sent: Thu 2/22/2007 3:42 AM
To: Radisky, Evette S. Ph.D.
Cc: CCP4BB@jiscmail.ac.uk
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)
>
---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail [EMAIL PROTECTED]
