Thank you all for the guidance. Avisek
On Mon, Mar 2, 2015 at 4:24 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > Dear Avisek, > > did you try shelxd for substructure solution? I think that it tries to > avoid the Uranium solution. There are a couple of caveats with soaks, > e.g. you are not sure about the number of sites and their occupancies. > Occupancies are refined by shelxd, and you can test a few number of > search sites - shelxd has a certain tolerance with respect to the number > of sites. Do you have a native data set, too? Maybe you could try SIRAS > instead of SAD for better phases? > > If you feel unfamiliar with shelxc / shelxd shelxe , you can use the GUI > through ccp4i, or also hkl2map which guide you through the process. > > Note that autotracing may not work well at 3A resolution. > > Best regards, > Tim > > On 02/23/2015 02:29 PM, Avisek Mondal wrote: > > Dear all, > > I am trying to phase a large novel structure of 150 kDa with P21 space > > group. So far I have collected 3.0A datasets from iodinated derivatives > in > > Cu-K alpha. In SAD phasing I got 0.745 figure of merit (FOM) and LLG > about > > 476208.27 (sites in inverse hand gave the same FOM and LLG),by Phenix > > Phaser-EP. But i am seeing monstrous peak from the substructure solution, > > it seems that all phases merge into huge fourier peak (like Urenium-atom > > solution and Fourier truncation ripples; Ref.Bernerd and Rupp) .But it is > > clear that the iodine has incorporated into the proteins lysine residues > > where the large electron density has been seen (from partial molecular > > replacement solution). Would anyone be able to advise me on how it'd be > > best to improve my phases/density given the limitations of the data? it > > will be very helpful for me as a learner. > > > > Avisek > > > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > >
