Hi Pu, Looks like I'm a little late with my reply, but if you have a similar problem again you could try "EMMA", e.g. via this web interface:
http://cci.lbl.gov/cctbx/emma.html Pasting in your unit cell, space group and coordinates, I got the output below. It means the two sets of heavy atoms are equivalent under the symmetry of the substructure search space (http://cci.lbl.gov/~rwgk/my_papers/iucr/ba5051_reprint.pdf). Ralf Tolerance: 3.0 Reference model Unit cell: (61, 137.7, 142.17, 90, 90, 90) Space group: P 21 21 21 (No. 19) Hg1 0.5984 0.5673 0.0980 Hg2 0.9020 0.5702 -0.0989 Hg3 0.7276 0.5944 -0.2403 ############################################################################### Model 2 Unit cell: (61, 137.7, 142.17, 90, 90, 90) Space group: P 21 21 21 (No. 19) Hg1 0.5987 0.4322 0.0984 Hg2 0.9015 0.4302 -0.0984 Hg3 0.7274 0.4068 -0.2403 ............................................................................... Match summary: Operator: rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} translation: {0, 0.5, 0.5} rms coordinate differences: 0.12 Pairs: 3 Hg1 Hg1 0.085 Hg2 Hg2 0.085 Hg3 Hg3 0.168 Singles model 1: 0 Singles model 2: 0 ############################################################################### ________________________________ ----- Original Message ---- From: Pu Gao <ga...@moon.ibp.ac.cn> To: CCP4BB@JISCMAIL.AC.UK Sent: Thu, August 19, 2010 9:35:48 PM Subject: [ccp4bb] Heavy atom sites? 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
