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Probably easiest to start again with the correct FreeR You can perturnb the strucures pdbset xyzin MR.pdb xyzout- MRshaken.pdb NOISE 0.3 That moves everything a bit. Or if you do enough cyles the FreeR should increase steadily to a sensible value then level off Easiest to use the GUI and click the button - add FreeR from existing mtz file! Eleanor Harry M. Greenblatt wrote: > BS"D > > Dear All, > > Someone has come to ask my opinion about some inhibitor-protein > complexes they have refined, isomorphous with a known native structure > (P21212). After a short look at the statistics, I became suspicious > about the R-free selection for the new complexes. Indeed, the person > was not careful about taking the the same R-free set as the native. > Each complex had a new R-free set, and Refmac was used (i.e., they did > not benefit from simulated annealing, which according to some would > have saved the situation). So the difference between R and Rfree is > about 2-3% for each structure, since the structures are biased to a > large fraction of the new Rfree set. Technically, the process was > incorrect, but how can they remedy the situation (short of starting > from scratch with the proper Rfree set)? Run simulated annealing now, > and then a round of Refmac? > > Thanks, > > Harry > > ------------------------------------------------------------------------- > > Harry M. Greenblatt > > Staff Scientist > > Dept of Structural Biology [log in to unmask] > <mailto:[log in to unmask]> > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > >