well - Q1. I think you can observe it.. And there is no format problems in modelling several residues as conformation A and B Eleanor
On 16 May 2017 at 19:33, Sam Tang <[email protected]> wrote: > 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 > > >
