In addition to the remarks of Mark and Tim, could you make sure that you are refining in Refmac with the correct flag for the Rfree set (value = 0)? In Phenix, this is the opposite: the value is 1 for test reflections and 0 for work reflections. So going from a PHENIX environment to Refmac, you might well be refining against your small fraction of test reflections. I have seen this give spurious density features (obviously) and serious model bias.
Cheers Jonathan Ghent University On 08 Dec 2011, at 18:50, Mark J van Raaij wrote: > are you sure that you are using the original input intensities for the REFMAC > map calculation (and the refinement run) and not the output ones of the > (previous) run? > if you are not, you may have model bias, and Rfree can be fooled, especially > with NCS (if you have it). > > - or perhaps anisotropic B-factor refinement (if you are using it), works > better in REFMAC than PHENIX? > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/content/research/macromolecular/mvraaij > > > > > > On 8 Dec 2011, at 18:36, Christopher Browning wrote: > >> Dear All, >> >> Question: Has anybody ever refined the same structure using PHENIX and >> then tried REFMAC to see what happens? >> >> I did and I stumbled on something funny. I'm refining a structure at >> 1.1A resolution which was solved with Iodine phasing using PHENIX >> AutoSolve. Got a great map and the structure was built almost >> completely. I had to build a few residues myself, and using the >> published sequence, I started filling in the residues, but as I came >> nearer the N-terminus, it looked like the density did not match residues >> from the sequence. I kept the residues as in the sequence, but as you >> can see from the PHENIX refined picture (below is the link) it still >> looks like the amino acid sequence in the crystal does not match the >> published protein sequence. >> >> Out of interest I refined the same file in REFMAC, and now the electron >> density is correct, and the sequence of the amino acids in the crystal >> matches the published sequence (see link for picture below). Not only >> that..... my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). >> >> I've also refined the occupancies of the iodide, however the the output >> FO-FC map from PHENIX complains and the REFMAC map is fine..... >> >> How can this be and what causes this? >> >> Link for the pictures: >> Both maps are at identical Sigma levels in both pictures. >> PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png >> REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png >> >> Cheers, >> >> Chris Browning >> >> >> >> -- >> Dr. Christopher Browning >> Post-Doctor to Prof. Petr Leiman >> EPFL >> BSP-416 >> 1015 Lausanne >> Switzerland >> Tel: 0041 (0) 02 16 93 04 40
