Hi, not knowing other details, the most naive guess is that this may be a footprint of mask-based bulk-solvent model. Next one is that you are contouring at too low/high level (note, sometimes, if, for instance, solvent content is high, you need to look above/below 3sigma). Of course, there could be gazillions of other causes.
Pavel On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven <[email protected]> wrote: > Hi everyone, > I was recently looking at the following structure deposited in the > PDB: 4g1m. Overall, the structure fits nicely the density, but the map > shows large red blobs inside some of the domains (negative density > disappears around 5 sigma). Could this be due to an excessive low R > factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a > resolution of 2.85 A? >
