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Re: preparing NCS-mask in DMMULTI

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On Fri, 12 Mar 1999 burkhardp@ubaclu.unibas.ch wrote:

> I want to run multiple crystal averaging. How do I set up the ncs-masks 
> properly. I have a first crystal form with 8-fold NCS and a second
> crystal form with 2-fold NCS (of the same domain). The space groups
> differ.

you want one mask covering a monomer, along with the the operators to move
density from that reference monomer to all the other monomers in both
crystal forms.  DMMULTI can automatically generate the masks for the other
monomers from this information. the NCS operators you want should work on
orthogonal Angstrom coordinates, so that crossing from one crystal form to
another is no problem.

hopefully you can see the molecular boundaries and approximate layout of
the monomers in the NCS multimer?  if things are fuzzy, start with a
sphere, and improve the mask after the averaging improves the density.
later you could use some sort of BONES skeletonization, convert them to
fake PDB coordinates with BONES2PDB, then use the PDB file for

if you are having trouble establishing the monomer boundaries, it may be
simpler to do some averaging within one xtal form or the other until your
density improves a bit. 8-fold NCS averaging alone would still be pretty
see the DM documentation for info on the "NCSMASK OVERLAP" option; you may
use a mask covering all monomers within a proper NCS multimer, instead of
covering just one monomer if you can figure this out.

the NCSMASK "MONOMER" function will not work over 2 crystal forms, in fact
it will only work if your NCS symmetry is simple N-fold rotational
symmetry (for your 8-fold crystal form, this would mean 8-fold rotational
symmetry instead of 2 x 4 symmetry, or whatever).  if you want to do any
mask trimming or overlap removal, work only within one crystal form.

if you feel a need to refine the NCS operators before running DMMULTI, you
can do this within a crystal form using IMP from the Upsalla RAVE package,
and from one crystal form to another using MAVE of the same package.  if
you do so, beware the differences in matrix format between CCP4 and RAVE.
See the documentation about this.  The best test for any matrix is to
apply it to coordinates and see if they end up where they should.

it should not matter what spacegroup is written to the mask header.
DMMULTI should read it in as just a chunk of density.

i am currently on my 3rd application of multi-crystal averaging; once did
6 + 2 averaging for horseradish peroxidase.  i still use my own averaging
software MAGICSQUASH instead of DMMULTI, but the principles are the same.

good luck, and check out the quote below:

"multi-crystal averaging... is the greatest phasing tool in the world!
 Knocks MAD into a cocked hat."  -  Eleanor Dodson
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine