My money is on the the wrong test set (as Jonathan Elegheert suggested). I have seen this several times with newbies, when the test set is created by phenix. It does it the "xplor-way". When it comes to the free set, refmac defaults to 0, phenix tries to be intelligent (i.e. if 1/0 it uses 1, if more 0/1/2... it uses 0). Additionally, refmac (and I think phenix) produces Fc filled maps. So if you swap R/freeR reflections, the maps always look spectacular, as they essentially are Fcalc maps. Inspection of the logfiles should help: #of reflections free and #of reflections for refinement are reported by both programs, and IIRC, you should get a warning that your free-R-set is not sensible. One way out is to /always/ use ccp4 to assign the test-set, then both programs run fine. Otherwise you have to explicitly tell refmac to use "1" as the test reflections.
HTH, Jens On Thu, 2011-12-08 at 18:36 +0100, 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 > > >
