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It is likely to be a difference in the scaling. Can you merge the two data sets, run scaleit or something to analyse the difference v resolution? Eleanor Sabine Schneider wrote: > Hello everyone, > > I am puzzled about differences I see when I refine the very same > structure against data processed with xscale or scala. > > I got data to 2.55A from a protein-ligand complex. The data were > processed with xds/xscale (1) or xds/scala (2) > Free R was imported from a previously solved structure with a > different ligand, first to (1) and from there to (2). > After MR and refinement (Refmac/Phenix), I get some difference density > peaks (a bit pos and neg), near the ligand when I refine against (1) > and it converges more or less around R/Rfree of 20.9 and 24.8. I do > not get these pos and negative density blobs when I refine the same > coordinates against (2), with a tiny bit higher R/Rfree of 21.6/26.1? > So the data processed with scala, where I get slightly better > refinement statistics, I end up with some pos/neg density peaks. They > don't show up when I apply a high resolution cut-off of 2.65A during > refinement. > > Symmetry is orthorhombic and the statistics are OK (Rsym 0.09 and 0.38 > in highest shell, redundancy ~5, I/sigI =1.9, mean I/sigI = 5.2 ) and > in both files appear to be more or less the same number of reflections. > > I also did simulated annealing, omitting the region around the ligand > in a 15A radius and the density is nicely coming up. But it doesn't > make a difference: after refinement I always end up with the result as > discribed above? And there isn't really a difference between the two > structures in the end. > > Has anyone an idea whats going on? > > Sabine > >