when these kind of things occur to me it always is a silly mistake like: - occupancies of the new residues set to 0.0 - reading in the old pdb-file when running refmac instead of the new one - calculating the map with the old refmac output instead of the new output - reading in and/or displaying the old map in coot instead of the new map but I guess you checked all this...
Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1 On 1 Mar 2011, at 17:32, Judith Reeks wrote: > Dear All, > > I am currently refining a structure using the latest experimental version of > Refmac (5.6) and there seems to be a problem with my Fo-Fc map. There is a > region where I have fitted residues to the electron density but after > refinement there is still positive electron density assigned to the region > despite the fact that residues fit the electron density (see link below for a > screenshot). Multiple rounds of refinement have yet to get rid of this > problem. I have checked the PDB file and there does not appear to be any > problems with this region. Has anybody seen something like this before? > > http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png > > Regards, > > Judith Reeks > [email protected] > School of Chemistry > University of St Andrews
