Hi, It's not uncommon for pseudosymmetry to be found together with twinning, and the presence of pseudosymmetry perturbs the statistics used to test for twinning. In that circumstance, as Phil suggests, a really good way to see what is going on is to take the lower symmetry solution and see if it really obeys higher symmetry, but you can do that either with coordinates or calculated structure factors.
Your NCS matrix specifies a 2-fold rotation around an axis that is about 1 degree off the x axis. Whether that 1 degree matters or not depends on how precisely the molecules are placed in the MR solution. If 30.8649 is precisely half of the a-cell edge, then this corresponds to a 2(1) screw axis, but whether or not that is crystallographic depends on whether the origin of that axis is in the right place relative to the 2(1) you're assuming is correct. Working all that out from coordinates can be a bit of a challenge, which will really have you hitting the books! The other way we've approached this kind of problem is to take the Fcalcs from an MR model (usually solved in P1 if possible to avoid making any assumptions about which symmetry operators are correct) and then use either pointless or xtriage to see if those Fcalcs obey higher symmetry. Another good approach is to use the zanuda program in the CCP4 suite, which is designed to answer questions about pseudosymmetry and other related problems. Good luck! Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 15 Oct 2013, at 22:31, Yarrow Madrona <amadr...@uci.edu> wrote: > 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
