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Dear Tim, I agree with you completely. The question then becomes why does the automatic weighting scheme in refmac allow R and R-free to run away from each other by 8% in a 1.1 A resolution structure? Petr On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote: > -----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-----