-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Wenhua,
a large gap between R1 and Rfree is often inficative for overfitting. Take a look at the following: - - how many water molecules are there in total? Do they all chamically make sense, do some of them have large B-values? Water molecules are the trash bin of any crystallographic model: it is easy to drop the R1-value by adding water molecules. - - do you have a good geometry (run molprobity)? Otherwise you should tighten the weight adding more weight to the geometry restraints. Having said this I noticed that refmac5 has greatly improved over the passed two years with respect to automated weighting. - - Do your B-values vary reasonably? There is a utility in coot displaying the B-factor variance along your structure. Again, if you are using refmac5, there should not be much of a problem here. - - Check the occupancies of your atoms. Recently I noticed a substantial number of PDB entries with occupancies varying within a molecule, sometimes even within one residue. This make no sense to me at all and again, even if there were a plausible explanation (e.g. hydrogen exchange in water molecules for neutron structures), the limited resolution of most structures in the PDB does not justify this variation. Best, Tim On 11/26/2013 09:49 AM, Wenhua Zhang wrote: > Good Morning to ALL, > > I encountered large gaps between R-factor and R-free, eg. 10% and > 11%, during refining several structures with either Refmac or > Phenix.refine. The data were reduced and scaled at resolution with > I/SIGMA higher than 2.3. The model fits and density pretty well > despite a few side chains missing density. > > I may ask for the reasons that result in such large difference > between R and R free and some ways to examine and improve the > refinement. > > Thanks in advance > > Wenhua > > Univ. Paris-Sud XI, Orsay > > > On 11/25/2013 6:03 PM, Beatrice Vallone wrote: >> Please check the announcement for 2014 ESRF Users' Meeting & >> Associated Structural Biology Workshop. >> >> Invitation to the 2014 ESRF Users' Meeting & Associated Workshops >> to meet and discuss with fellow users, get inspired, establish >> new scientific collaborations and learn about future >> opportunities offered by the ESRF for your research. >> >> Workshop on*"Structural Biology at ESRF: Past, Present & Future >> <http://www.esrf.eu/home/events/conferences/um2014/structural-biology-workshops.html>"* >> >> >> 3 - 5 February >> >> The Plenary Meeting will feature: >> >> * 5 plenary lectures by world leading scientists covering a >> large spectrum of ESRF activities; * a presentation on the status >> of the facility and on the progress of the Upgrade Programme; * a >> talk by the winner of the prestigious "ESRF Young Scientist >> Award"; * a poster session; * a banquet, with awards to the ESRF >> Young Scientist Award and for the best poster >> >> Programs for the Meeting and Workshops are available at: >> >> http://www.esrf.eu/home/events/conferences/um2014.html >> >> Regards to all, >> >> Beatrice Vallone ESRF User Organization Committee >> >> >> > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSlGZeUxlJ7aRr7hoRAhNwAJ9F3utsgf6uNMW80j5by1RHbyTAtQCfYkfV 2Xsl1cLsB4BPYuabWOqouHM= =NI2B -----END PGP SIGNATURE-----
