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
