Hi Phil,
Thanks for your help.
I ran a "Find-NCS" routine in the phenix package. It came up with what I
pasted below:
I am assuming the the first rotation matrix is just the identity. I need
to read more to understand rotation matrices but I think the second one
should have only a single -1 to account for a possible perfect 2(1) screw
axis between the two subunits in the P21 asymetric unit. I am not sure why
there are two -1 values. I may be way off in my interpretation in which
case I will go read some more. I will also try what you suggested. Thanks.
-Yarrow
NCS operator using PDB
#1 new_operator
rota_matrix 1.0000 0.0000 0.0000
rota_matrix 0.0000 1.0000 0.0000
rota_matrix 0.0000 0.0000 1.0000
tran_orth 0.0000 0.0000 0.0000
center_orth 17.7201 1.4604 71.4860
RMSD = 0
(Is this the identity?)
#2 new_operator
rota_matrix 0.9994 -0.0259 0.0250
rota_matrix -0.0260 -0.9997 0.0018
rota_matrix 0.0249 -0.0025 -0.9997
tran_orth -30.8649 -11.9694 166.9271
> Hello Yarrow,
>
> Since you have a refined molecular replacement solution I recommend
> using that rather than global intensity statistics.
>
> Obviously if you solve in P21 and it's really P212121 you should have
> twice the number of molecules in the asymmetric unit and one half of the
> P21 asymmetric unit should be identical to the other half.
>
> Since you've got decent resolution I think you can determine the real
> situation for yourself: one approach would be to test to see if you can
> symmetrize the P21 asymmetric unit so that the two halves are identical.
> You could do this via stiff NCS restraints (cartesian would be better
> than dihedral). After all the relative XYZs and even B-factors would be
> more or less identical if you've rescaled a P212121 crystal form in P21.
> If something violates the NCS than it can't really be P212121.
>
> Alternatively you can look for clear/obvious symmetry breaking between
> the two halves: different side-chain rotamers for surface side-chains
> for example. If you've got an ordered, systematic, difference in
> electron density between the two halves of the asymmetric unit in P21
> then that's a basis for describing it as P21 rather than P212121.
> However if the two halves look nearly identical, down to equivalent
> water molecule densities, then you've got no experimental evidence that
> P21 with 2x molecules generates a better model than P212121 than 1x
> molecules. An averaging program would show very high correlation
> between the two halves of the P21 asymmetric unit if it was really
> P212121 and you could overlap the maps corresponding to the different
> monomers using those programs.
>
> Phil Jeffrey
> Princeton
>
>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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