I would also ask what is the actual goal in refining the occupancy of the ligand?
While I agree wholeheartedly with George, the B-factors will adequately model a lower ligand occupancy. Usually the question you want to resolve is "Is the ligand really bound in the active site, or is this an artifact of the model?" However, if you're trying to resolve a static disorder in an active site, say half ligand and half solvent occupancies, then refining the ligand occupancy can be useful. Thus, what you really need to do is compare a refinement with just B-factors and full occupancies vs. a refinement with the added restrained ligand occupancy variable, in some sort of R-test, comparison of GOF, etc. Does it really improve the model? Bernie Santarsiero On Mon, December 17, 2007 8:43 am, George M. Sheldrick wrote: > I thought that I would never have to disagree with both Eleanor and > Tassos in the same email, let alone risk being burnt at a stake as a > heretic for doubting the Gospel according to Kleywegt, but in my > experience, given the very fortunate position that you have data to > 1.5A, the refinement of one occupancy parameter for the whole ligand > (e.g. one SHELX free variable) will be rather well defined provided > that sensible restraints are applied to the B-values. A common variant > of this for ligands or side-chains is to refine one component with > occupancy p and an alternative component or conformation with an > occupancy 1-p, still only requiring the addition of ONE refinable > parameter. If you are using SHELX and your ligand (or part of it) > happens to be rigid, the rigid group refinement offers a further > way of keeping the number of refinable parameters down. The Dundee > PRODRG server is an excellent source of ligand geometries and > restraints for such refinements. > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-2582 > > > On Mon, 17 Dec 2007, Anastassis Perrakis wrote: > >> > I have already changed occupancies as Eleanor mentioned, and got >> > approximate values. But my hope is to try to get much precise ones if >> > possible. >> > >> I never expected to preach the 'Kleywegt Gospel' in the ccp4bb, >> but in this case what you need is more accurate answers, not more >> precise ones >> (or better both, but precision alone can be a problem, and you can >> easily get >> 'precise' but inaccurate data easily by making the wrong assumptions >> in your experiment) >> >> http://en.wikipedia.org/wiki/Accuracy >> >> > I have heard from my colleague SHELX can refine occupancies, and >> > got its license. I'll next try SHELX. >> >> I think that phenix.refine can also do occupancies ? >> The problem is not if the program can do it, but if at your specific >> case >> you have enough information to do that in a meaningful way. >> >> For a soaking experiment and 1.5 A data, I would say that Eleanor's >> suggestion >> of tuning Occ based on B, is as close as you would get, accurate enough >> given >> the data, >> although not necessarily too precise. >> >> Tassos >> >
