Thank you Dale, I will "hit-the-books" to better the rotation matrices. I am concluding from all of this that the space group is indeed P212121. So I still wonder why I have some outliers in the intensity stats for the two additional screw axis and why R and Rfree both drop by 5% when I apply a twin law to refinement in P21.
Thanks for your help. -Yarrow > Since Phil is no doubt in bed, I'll answer the easier part. Your > second matrix is nearly the equivalent position (x,-y,-z). This > is a two-fold rotation about the x axis. You also have a translation > of about 31 A along x so if your A cell edge is about 62 A you have > a 2_1 screw. > > Dale Tronrud > > On 10/15/2013 12:29 PM, Yarrow Madrona wrote: >> 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
