Thanks, Poul! How could I change the scale of the data intensities by a factor 2-3? Do I need to change it in scaleit or to change it in mlphare? Is that always necessary to make the occupancy of the major site to become ~1? I'll try this. I use phenix to detect the twin effect, the results turned out be no twin in my case. Any suggestion on this?
Thanks so much! 2009/2/21 Poul Nissen <[email protected]> > Hi alphar~ > Check the sites you get from anomalous difference Fouriers and stick to > those as your correct HA sites. At the same time you may consider not to > refine the HA substructure on the anomalous differences but merely using the > isomorphous differences. Maybe you need to change the scale of your data > intensities by a factor 2-3 to get the major sites at an occupancy of ~1 in > the SIR/MIR refinement. > > Finally R32/R3 space groups are prone to twinning problems in which case > the MIRAS phasing will be a nightmare explaining your current pathologies > > Poul > > On 21/02/2009, at 04.11, Fengyun Ni wrote: > > Hi everyone! >> I have a question on my poor MIR map. >> >> Four datasets (two AU and two HG) were used for phasing upto 3 A >> resolution in my case. I could locate several heavy atom sites for each >> dataset with occupancy finally refined to about 0.3 to 0.4, and with B value >> refined to about 50 to 80. I did not include the anomalous data because once >> I refine against anomalous data, the anomalous occupancy was only about >> 0.02, and even smaller as 0.004 for some sites. I guess the anomalous data >> are not good enough, so I did not use them right now (Could I do this? Or >> must I include them somehow?). >> >> The FOM I got is about 0.6, the Cullis-R factors were about 0.6 for all >> four data sets, and the phasing power was about 2.5 in each dataset. After I >> did the density modification, the FOM could increas to about 0.8. >> >> My problem is that the protein should form a long helix structure as >> indicated by other homology protein, but in the map after density >> modification, the densities are not consecutive though the overall shape >> seemed to be a long helix. The good thing is that some short helix-like >> densities could be observed in the current map, but they are not connected >> to each other. >> >> Right now, I am totally lost whether I should believe in the mir-map I >> have. Could I improve this map with some other method? Or should I re-do the >> phasing? >> BTW, the space group for my crystal is R3 or R32 with a=50, b=50, c=380, >> alpha=90, beta=90 and gamma=120. The c-axis is much longer than a- and >> b-axis, so the reflection data suffered from the anisotroy effect. >> >> Any suggestion on my phasing problem is welcome. >> >> -- >> Alphar Ni >> Call me alphar~ >> :) >> > > -- Fengyun Ni Call me alphar~ :)
