Hi Pu Obviously your SAD & SIRAS solutions can't both be right, one must have the inverted handedness: I would guess it's the SIRAS solution that's wrong, since the SAD solution seems to have given you an interpretable map. The reason for getting the wrong hand in the SIRAS case is probably that the anomalous contribution is smaller relatively, so is unable to discriminate the solutions. But what makes you think that the SIRAS solution you (or the program) have chosen is correct, in particular how do the peak heights in the HA-phased map compare for the SIRAS solution inverted through the origin, i.e. the SAD solution?
-- Ian On Fri, Aug 20, 2010 at 5:35 AM, Pu Gao <ga...@moon.ibp.ac.cn> wrote: > Hi all, > > I recently solved a structure using SAD or SIRAS successfully (refinement > using native data). But I came across some questions about the heave atom > (Hg) sites. SG : P212121. Cell: 61.000 137.700 142.170 90.00 90.00 90.00 > (native and derivative are very similar). > > 1. I used shelxD finding the Hg sites, but got different results from SAD and > SIRAS. Here paste the first 3 sites: > X Y Z X > Y Z > (fractional) (orthogonal) > SAD: > Hg1 0.598389 0.567345 0.098041 36.759 78.146 13.983 > Hg2 0.901955 0.570168 -0.098881 55.407 78.535 -14.102 > Hg3 0.727585 0.594368 -0.240330 44.696 81.868 -34.276 > > SIRAS: > Hg1 0.598717 0.432159 0.098363 36.522 59.508 13.984 > Hg2 0.901527 0.430199 -0.098437 54.993 59.238 -13.995 > Hg3 0.727432 0.406845 -0.240253 44.373 56.023 -34.157 > > It seems there is a symmetry plane m(x,1/2,z) between SAD sites and SIRAS > sites. The above HA coordinates were in real space not the partterson space, > right? So could someone tell me why there is a m? > PS: the Harker section plots (FFT for patterson in CCP4) of difference > patterson and ano-difference patterson are very similar. > > 2. I put the Hg sites caculated by shelxD (say, the SAD sites) to SHARP and > got the density map (looks very good). RESOLVE was used to autobuild the > model. The Fo-Fc map (Fo from Hg-data, Fc from the model after refinement) at > sig>5 obviously showed the Hg sites (around Cys). But the heave atom > coordinates (from shelxD or sharp) didn't match the Fo-Fc density. I don't > know why is that? Dose it bucause the coordinate system mismatch? > > Any help would be much appreciated. > > Thanks, > > Pu >
