-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Christopher,
if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be looking at an electron density map with strong model bias, i.e. the map shows the features of the model and not of the data. Although at 1.1A resolution this seems quite unlikely, but that's what might explain this great gap between R and Rfree. Tim On 12/08/2011 06:36 PM, 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 Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO4PjgUxlJ7aRr7hoRAszXAKCNmTZvCVaDUm6v3lQjp051H+ilDgCgxd1l as9CcWEseq9uEV8qMZsOfsg= =KKUr -----END PGP SIGNATURE-----
