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Re: [ccp4bb]: NCS averaging

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On Wed, 4 Oct 2000, Jinsong Liu wrote:

> What is the easiest (or best) way to get a NCS matix out of a phased
> map?

does "2 Se position" mean 2 per dimer or 2 per monomer?

first off, if you have a poor MR model, you could try Randy Read's max
likelihood MR program.  it worked for me.

second, for the MAD phases, are they any good at all or could you be
looking at artifact?  this is the second case i've heard of in the last
month where there appears to be 2 molecules in the ASU with a
translation-only operator.

get the best non-averaged map you can from the MAD phases. i would try
SHARP & SOLOMON.  you could also try Kam Zhang's version of SQUASH with
double histogram matching.  use a range of solvent values, if you miss on
that it will screw up any of these methods.  try both hands with the MAD 
Se sites (x,y,z vs. -x,-y,-z).  GIGO.

now, is your map any good?  can you really see the protein envelope?
does the stuff inside the envelope appear to be protein?  can you see any
helices or sheets?
if you use the MAD phases with the Pt amplitude differences in a Fourier,
do the Pt sites show up, or did you merely pick your Pt sites form a
Patterson map?

supposing your map does actually look promising, you could try direct
visual methods - load up the map in a viewing program (TOM, O,
whatever) along with all your known sites; Se, Pt, if there is secondary
structure perhaps a skeletonized object. move the sites corresponding to
one monomer onto the second and print out the matrix.  you can use the
Uppsala program IMP to refine a rough matrix.

no matter what method you use to find an NCS matrix, I would verify it by
applying the matrix to some actual coordinates (e.g. your Se sites) and
checking whether the result is where it should be.


"The Wrong Hat is like wearing an enormous sign, duct-taped to a plumber's
helper stuck to your head, that says, "I'm a moron."  - Mimi Pond
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine