Dear all Sorry for the slightly off-topic thread.
We are lucky enough to have recently solved a protein-ligand structure in P1 space to 2.4 A by molecular replacement using the apo-protein as model. The protein is known to have a flexible loop region of about 20 amino acid long. In the apo-protein (model), density for > half of this loop are not seen. It seems interesting to us that, in the complex structure, although still incomplete, there seems to be loop densities at two distinct conformations (named up and down, which point to opposite directions almost 120 degree) -- when we fit the loop to the up conformation, difference map shows green blots at the down conformation, and vice versa. What we feel puzzled are: (1) Is it possible, at this resolution, for the two conformations be observed? Or is there any similar case we can make reference to? (2) If the densities below to two conformations of the loop, how should we model it? Add alternate conformation function in Coot doesn't seem suitable. Or should we make up (and eventually deposit) two models showcasing the two conformations? Many thanks in advance for your attention! Regards Sam
