You have to build the model you actually believe matches what is in the crystal. Do you believe that each amino acid is occupying two conformations independent of its neighbors? I wouldn't go that way. I would start with an apo conformation, labeled with 'g', and a holo conformation including the ligand, labeled with 'h', and allow all of 'g's one occupancy value, and the 'h's another, and insist that they sum to 1.0. You may have to build water molecules in the binding site of 'g' that are displaced by the ligand in 'h'.
If this, simplest of models, doesn't do the trick you have to be lead by your difference maps and chemical intuition to devise more complex models. Select the simplest model that makes sense and fits your data. It would be interesting to see if you can find a program that would allow you to restrain the ncs of the second protein chain and the 'h' conformation of your mixed model, leaving the 'g' conformation unrestrained by ncs. Dale Tronrud P.S. I'm avoiding the use of 'A' and 'B' alt locs because these are routinely used when splitting side chains but are almost never intended to imply that all 'A's are coordinated with each other and all 'B's are likewise. To be proper, the reuse of alt loc codes for unrelated conformations should not be allowed, but there are simply not enough letters to allow the rule to be enforced. On 08/07/12 07:59, Kendall Nettles wrote: > Hi, > We have a structure with the ligand showing two overlapping conformers. > When we refine it with both conformers separately, it is pretty clear > that there are substantial differences in the protein as a result, for > about a third of the protein chain. My question is, would it be better > to try to define alternate conformers for those specific regions, or > would it be OK to refine with two entire alternate protein chains? There > is also a second protein chain that shows only a single binding mode for > the ligand. It's a 2.0 angstrom structure. The yellow 2Fo-Fc map goes > with the green model in the attached pic. Also, do we want to let each > amino acid have its own occupancy? or should one ligand copy and one > chain all have the same occupancy? I'm leaning towards the latter since > the differences should be directly tied to the ligand binding mode. > Kendall Nettles
