What do you mean - running REFMAC directly on the output file? Are you sure you have the same space group given in the mtz file and the PDB file? If the MR has placed your structure in P32 say, nd the input mtz has SG P31, you need to change the mtz header to include the now-known SG. There are various ways given on the Reflection Utility task in the GUI. Eleanor On 30 Jul 2012, at 11:04, Damian Niegowski wrote:
> Dear all, > > I am currently trying to refine co-crystallized ligand structures at 2.8-3.4 > Å resolution. After initial molecular replacement the density in the maps, > both 2Fo-Fc and Fo-Fc looks good and the ligand seams to have > bound. However after running Refmac directly on the output files the maps get > much worse. I am using a "clean" pdb, without ligand or water for the Phaser > and subsequent Refmac runs. > Also when refining with the ligand in the B factors are a lot higher for the > ligand then the surrounding residues, only when lowering the occupancy to > 0.7-0.8 for the ligand the B factors look > better. Is that acceptable to do at this resolution? R-free is in the > 0.24-0.27 range. There is only a marginal change in R-free with the addition > of ligand. TLS refinement seams to help alot for overall > R values but does not improve the maps. I have also tried Phenix with > simulated annealing, rigid body and reference structures. > So the question is how best to proceed with refinement at the rather low > resolution?? > > Regards, > > Damian > > Damian Niegowski Ph.D. > Institute of Medical Biochemistry and Biophysics > Karolinska Institutet > Scheeles väg 2 > 171 77 STOCKHOLM > e-mail: damian.niegow...@ki.se > phone: 0046 8 524 876 33 > fax: 0046 8 736 04 39
