That is very pleasing! Ramachandran vindicated yet again.. Eleanor On 2 October 2017 at 10:31, Meytal Galilee <meytal.gali...@gmail.com> wrote:
> Dear all, > Many thanks for your responses. > Indeed the peptide was wrong handed, flipping the peptide chain fixed all > my outliers issues! > Thanks again! > Meytal > > 2017-10-01 23:12 GMT+03:00 Eleanor Dodson <eleanor.dod...@york.ac.uk>: > >> 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 >> > >> > > > > -- > Meytal Galilee >
