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Re: [ccp4bb] Low resolution model building |
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CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 12 May 2007Subject: Re: Low resolution model building From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU Date: 2007-05-12 Kolstoe S.E. wrote: >Dear ccp4bb, > >I am about to start model building a fairly low resolution structure (3A) with ten identical monomers in the asu, solved using MR. What I am thinking of doing is to build one monomer using some form of averaged NCS map, replicate and translate my one built monomer into the other nine positions, and then refine in refmac with tight NCS restraints. But I have a couple questions: > >1) Is this a sensible approach at this resolution? > > Yes >2) Which programs would people suggest I use for the ncs calculations, map averaging and final replication of my built monomer into the other nine positions? I see coot has an "ncs maps" function, but I also see a number of usf and ccp4 programs that all seem to do similar things. I am also confused as to the different formats that ncs operators seem to come in, and which programs read which formats. Could anyone suggest a "road-map" of programs I could use that would accept each others outputs and hence accomplish this feat? > > To perhaps safe you some time, you could start a Resolve job over the weekend and let the computer trace as much as possible of the backbone, the new Resolve 2.13 with it's build script is fairly good even at low resolution. It perhaps will be able to pick up the NCS and do some density modification while building. If you already have manually built as much as you possibly can, then you can go ahead and determine the NCS operators via e.g. Coot (superimpose chain A onto B), then generate a mask via NCSMASK for chain A only and use this mask in DM for e.g. 100 cycles of averaging while refining the NCS operators on the fly. Then look at the map and keep building manually. The NCS mask option in Coot does not perform density modification, it only superimposes electron densities from molecule A to molecule B or the other way round. That's also useful, as you can see which parts of your molecule actually follow NCS, by the amount of overlapping electron density at those regions from either map. Or by lack of density from the averaged map :-) If you have further questions feel free to contact me. Good luck, Jürgen >Thanks, > >Simon > > > -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 CCP4bb navigationCCP4bb <-- 2007 <-- May 2007 <-- 12 May 2007 |
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