-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Petr,
there may be a couple of reasons, e.g. - - your data are not really 1.1A, but you simply integrated a lot of noise - - you entered some odd command or another option which allows refmac5 such a deviation - - your model is incomplete - - surely several more. When a well tested program does something unexpected, it is usually the user and not the program which misbehaves... The optimisation of the weighting scheme is based on the geometry of the model and not one the gap between R and Rfree. Cheers, Tim On 12/08/2011 08:43 PM, Petr Leiman wrote: > 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: > > 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/ iD8DBQFO4cyCUxlJ7aRr7hoRAqDTAJkBsSEIp2bH7hZlB23LJadHL2VhVQCg0r38 LGVjgK1z29vPc5V4lUh74vw= =wP9n -----END PGP SIGNATURE-----
