This is hard to understand/impossible, at least in terms of simple 2fo-fc and fo-fc maps. We can think of a difference map as the difference between two maps, like fo-fc map = fo map - fc map. There is no model in the region, since you deleted it, so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc cannot be positive.
No, wait, there will be solvent, so Fc = Rho(solvent) Fo-Fc is negative, so Fo <Rho(solvent) 2Fo-Fc positive => 2Fo>Rho(solv) 2Fo > Fc > Fo Fo > 1/2 Fc So this would be possible if the density of your protein is less than that of the solvent but more than half that of the solvent. Partial occupancy? but where the protein is missing there would be solvent (in Fo if not in Fc), so you still couldn't get below density of the solvent. Maybe its a problem with the solvent model? On 10/11/2017 09:48 AM, Karsten Dreifus wrote:
Dear all, I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. Molrep (template with 70 % seq identity) finds three NCS molecules (the template model has only 1 chain as it is in different space group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried about model bias, so I just deleted chain C and re-ran the refinement. I observe that in the place of chain C, the DELFWT map in Coot shows negative density (red colour). Shouldnt the deleted regions show POSITIVE density (green colour)? The 2fo-fc map in the deleted region shows usual blue colour. I shook the 2chain model with Phenix simple dynamics and then ran refinement with same results. How do I verify the model is correct? Karsten
