Christopher, if you send me the input PDB and data files (off-list, of course) I will have a close look and then explain what exactly happens and why. I also promise to post the summary on this mailing list (without revealing the identity of your structure, of course). If you send me the command you used to run PHENIX, I will comment on that too.
Please send the files to my email address: pafon...@lbl.gov Pavel On Thu, Dec 8, 2011 at 9:36 AM, Christopher Browning < christopher.brown...@epfl.ch> 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 >
