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Assuming the favorable PHE alternate position is A and the unfavorable
alternate is B, could you assign the ligand to be alternate position A?
On Fri, 2006-03-17 at 15:49 +0100, Ekström Fredrik wrote:
> In chain A I have one residue (Phe) in two alternative conformations.
>
> In this area, a ligand is accommodated; let us assume for the
> discussion that the occupancy is 0.8.
>
> When the ligand is present, the Phe is in a conformation that can
> coordinate the ligand. The occupancy of this conformation is 0.8. In
> the pdb I label this conformation as APHE and the ligand as ALIG.
>
> Although the resolution is low, I have some density that implicates an
> alternative conformation of Phe (similar to apo). This conformation is
> not compatible with a ligand binding. The conformation is labelled
> BPHE in the pdb, and of course no ligand can be present with Phe is
> this conformation.
>
> In the refinement, the incompatibility between the apo conformation of
> Phe and the ligand mess things up!
> /Fredrik Ekström
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
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