Lijun Liu 's suggestion is sensible. And is there any possibility of twinning?
But I always thought that at least in REFMAC all A conformations were restrained as a set, and ditto for B C etc. So if the documentation is to be believed an A chain would be restrained as a unit. I don't think there is any way to force the occs of the A ligand and A chain to refine together but at 2.5A you wouldn't want to refine occs anyway I guess. Eleanor On 7 Aug 2012, at 19:22, Dale Tronrud wrote: > 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