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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:[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) > > > > --- 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 [log in to unmask]