That seems strange! You couldn't have built it in the wrong direction could you?
Or have bound a L-handed peptide? There are outliers which can be explained by interactions with other features but it would be very very unlikely that all the residues were outliers Eleanor On 1 October 2017 at 17:13, Dale Tronrud <de...@daletronrud.com> wrote: > Hi, > > Bond length and angle targets are defined based on the local > chemistry and apply equally to small and large molecules. The > Ramachandran distributions were defined via an examination of, > basically, tripeptides. Your peptide model must be consistent with > these prior observations to be considered reliable. If it is not there > is likely something seriously wrong with your interpretation. > > In addition, your model peptide must make chemically reasonable > interactions with its partner. You didn't describe this aspect of your > model, but this is equally critical in the evaluation of the model of a > bound ligand. > > In my opinion the most likely explanation is that multiple > conformations of the peptide are binding. Without seeing the density or > being able to examine the data it is hard to generate possibilities. > > Dale Tronrud > > On 10/1/2017 2:20 AM, Meytal Galilee wrote: > > Hi All, > > I have solved a structure of a protein bound to a short peptide (11 > > residues) at 1.9A. > > The peptide fits the map perfectly, however, all of its residues are > > either Ramachandran / bond length / angle outliers. > > Fixing any of these issues forces the peptide to misfit the map > > dramatically. > > Is anyone familiar with short peptides outliers? Are these issues common > > / acceptable? > > Does anyone have an idea or suggestion? > > Many Thanks, > > Meytal Galilee > > >
