Hi, Ed I am dealing the similar problem. I checked CNS qindividual.inp. But how do I refine one compound with two or more possible conformations (mainly due to one bond rotation), each of wihich has a different occupancy? Thanks in advance.
Joe On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTECTED]> wrote: > I think the correlation between occupancy and B-factor depends > also on the size of the ligand (relative to resolution). > Bob Stroud, I think, has estimated occupancy by comparing > the integrated electron density of the ligand with that of > a well-defined, isolated water (assumed to be at unit occuancy?). > > In principle the integrated electron density is not affected > by applying a B-factor, it is just spread out over a wider > area. In the case of a single atom at 3 A resolution, it > is spread out under the neighboring atoms and effectively > lost, so it is hard to distinguish high B-factor from low > occupancy. > In a large ligand most of the atoms are inside the ligand, > so their spread-out density remains inside the ligand > and gets counted in the integrated density. In that case > high B-factor has a very different effect than low occupancy, > as only the latter reduces the total electron density of > the ligand. > > During a previous reincarnation of this thread I did the > simple test of refining occupancy and B-factor for a > stretch of the protein (holding the rest of the protein > at unit occupancy) in CNS 1.1, and I felt the results > were quite satisfactory (don't have the specifics now). > > Ed > > 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 >
