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 >> >> > >
