Part of what is bothering me is that the density showed up at one exact point in the refinement, and I am currently testing what exactly it was that changed things. To me, the blob almost looks like a mask of the molecule, and there is very little 2Fo density, so that's weird. I am also really bothered that the R value is so low, and yet there's this huge blob. Something seems buggy to me. Also a clarification: the blob runs into a two-fold axis in the middle, so things get dodgy there too. I will let you know what I find out.
JPK On Thu, Oct 27, 2011 at 2:53 PM, David Briggs <[email protected]> wrote: > I agree with Rafael, > > From those pictures it looks like a sugar chain - maybe 2-3 > saccharides in a row. > > HTH > > D > ============================ > David C. Briggs PhD > Father, Structural Biologist and Sceptic > ============================ > University of Manchester E-mail: > [email protected] > ============================ > http://manchester.academia.edu/DavidBriggs (v.sensible) > http://xtaldave.wordpress.com/ (sensible) > http://xtaldave.posterous.com/ (less sensible) > Twitter: @xtaldave > Skype: DocDCB > ============================ > > > > On 27 October 2011 17:27, Jacob Keller <[email protected]> wrote: >> Dear Crystallographers, >> >> In the course of a reasonably smooth refinement, all of a sudden there >> is a huge worm-hole-type blob in the electron density (see pics). Has >> anyone seen this before? Is it some effect of the refinement >> over-fitting or something? For some background, resolution is 2.2Ang >> and there are 4mol/ASU, but one of them is markedly worse in terms of >> density than the rest, and appears to be in a non-crucial part of the >> lattice, as if just sitting in one of the interstices. R/Rfree is >> ~19.5/24.5. >> >> Jacob >> >> -- >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: [email protected] >> ******************************************* >> > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
