Hello all, I'm currently working on a structure which if I stub a certain side chain phenix/coot shows me a large green blob which looks strikingly similar to the side chain, when I put it in and run another refinement the blob turns red.
Basically I was just playing around and I changed the occupancy of the side chain and now there are no complaints. But I was thinking, should I haven changed the Bfactors instead? Should I have left well enough alone? If I lower the occupancy manually and do not include alternate confirmations have I introduced modelling bias? Could someone recommend some good articles I could read on exactly how to correctly fix this problem. Thanks, GM
