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Re: Masking

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> naismith@st-andrews.ac.uk wrote:
> > We have a dimer in the asu and have good matrices to relate the monomers
> > (straight 180 rotn). The starting map is to say the least a little poor.
> >
> > Is there a way to harness the averaging to generate a better map from
> > which to derive the solvent mask?
> >
> > Effectively a single run of maskless averaging.

How 'straight' is your 180 degree rotation?  Does it propogate through
the whole unit cell?  

If yes... 
Then you're talking about pseudo-symmetry?  I'd recommend going 
back and examining your space group.  Running your whole kit 'n
kabootle in both possibilities.

If no...
ie: if the ncs doesn't propogate through the whole unit cell, and doing 
an unmasked averaging, if possible, would average non-equivilent
Wouldn't want that!

> > (The ncs mask can be simply made by putting an atom of 40A radius at the
> > centroid of the heavy atom position. On our tests this is about as good
> > as a monomer mask)

Go back and check the symmetry. 

Eleanor J. Dodson wrote:
>  dm will generate itts own mask if you ask it to. You must give the
> sovent content and ask for NCSMASK NMER 2 ( see "advanced keywords"

I'd recommend several different solvent contents in steps of 10%.  If
have poor phases and your real solvent content is low, the masks will 
overlap with ones in the next asu over and the whole thing will become 
one huge channel that goes all the way though your crystal.  You can
at  your masks in Turbo or O to make sure they are actually solid bodies 
that superimpose on your electron density.

have fun

diane h peapus, phd
Chemistry & Chemical Bio		dp72@cornell.edu	
Cornell University
380 S.T.Olin Lab			+1-607-255-2174 (voice)
Ithaca, NY 14850  USA		+1-607-255-1227 (fax)