Hi Grant, sounds like you did the right thing (as far as I can guess given the amount of information you provided).
In a nutshell, both, B-factors and occupancies, model disorder. The difference is that occupancies model larger scale disorder (such as distinct conformations) than B-factors (smearing due to temperature vibrations, etc). Perhaps in you case the side chain has several conformations among which you can see only one, and therefore it's valid to model it with occupancy less than 1 (I presume you refined one occupancy per all atoms in that side chain). Pavel On Mon, Nov 19, 2012 at 3:36 PM, GRANT MILLS < [email protected]> wrote: > 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 >
