Hi Kolstoe,
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
