Dear Pavel, Also worth mentioning the obvious that the mathematical functional form of an occupancy and a B factor in its -ve exponential is very different BUT at lower resolutions they behave similarly. Thus higher resolution refinement allows an 'easier' determination of each parameter. Greetings, John
Prof John R Helliwell DSc On 19 Nov 2012, at 23:54, Pavel Afonine <pafon...@gmail.com> wrote: > 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 > <gdmi...@students.latrobe.edu.au> 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 >
