Re: Masking

[Edward Berry <eaberry@lbl.gov>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Fred. Vellieux wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> David J. Schuller wrote:
> 
> > there is no such thing as maskless averaging.
> 
> I do not agree with this statement. A properly conceived density averaging
> program will offer this possibility.

> So, for proper NCS (e.g. 2-fold) one can give an e.d. map centered on
> particle on which averaging is to be carried out and "do it" without a
> mask. The density for both zones 1 and 2, where the NCS applies, will
> improve by the averaging operation, and the density outside will
> deteriorate.
> 
I think you still need a mask, because non-crystallographic symmetry
is "local" symmetry. In your example, the region outside the proper
n-mer will include symmetry-related n-mers which will be obliterated,
the cell will no longer have the true symmetry, and calculated phases
will give bad density even for the n-mer that obeyed the ncs.

You could limit averaging (or phase calculation) to one asymmetric unit,
but an arbitrary asymmetric unit such as P212121 0-1 0-1 0-.25  will 
contain part of several multimers, only one of which obeys the operator.

So the mask is really to define the asymmetric unit. A fairly simple mask
made by starting with a sphere centered in the multimer and expanded by
repeated cycles of "grow" and overlap-trimming until it fills the asu
might suffice, but I wouldn't call this "maskless averaging"

Now I realize you might be talking about a single cycle of density averaging
with no mask, not calculating phases but using the improved density 
directly to make a mask to use in the next cycle. That sounds reasonable 
to me, what happened to the sym-related multimers wouldn't matter.

Happy averaging,
Ed

-- 
Edward A. Berry, MailStop 3-250
Lawrence Berkeley National Laboratory
1 Cyclotron Road, Berkeley, CA 94720
Phone: +1-510-486-4335
Fax: +1-510-486-6059
Jfax +1-530-323-9836 (you send fax, I receive email)
e-mail: EABerry@lbl.gov