Hi,
~1/3 of a chain that show substantial difference suggests a
possibility that may deserve a check---the symmetry is actually lower
and the 2 conformations belong to two occ=1 mols (unless the SG is
already P1).
I had a case that the apo SG was P1 and ligand-bound (soaked) SG was
P1 too but the binding made the data very well reducible to P2. When
refined with P2, I got something like you mentioned. When going back
with P1, everything turned to be clean, also R and Rfree were ~3% lower.
Lijun
On Aug 7, 2012, at 9:59 AM, 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
<coot.png>
