Hi Pavel, thanks for the explanation. Call me lazy as I have not read the reference yet - does it explain how the bulk-solvent is incorporated into the model so that it is not represented in FMODEL written by Phenix (see Simon's script for sftools)? My naive thinking is that the bulk solvent model add to FMODEL so that particularly the calculated low resolution reflections match better the measured ones. Best, Tim On 10/13/2014 08:21 PM, Pavel Afonine wrote:
Thanks Tim, yes missed this one!
Hi Simon,
the differences in R-factors you observe are most likely because we use improved bulk-solvent modeling and overall scaling procedure. This is described here:
Bulk-solvent and overall scaling revisited: faster calculations, improved results. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst. D69, 625-34 (2013).
Specifically, Figures 3-4 in this paper make your observations very expectable.
Other contributions to differences are discussed here:
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010).
Pavel
On 10/13/14 11:10 AM, Tim Gruene wrote:
Dear Simon,
I found this a very puzzling observation and given the high throughput of this board, it is likewise puzzling you have not received a reply yet - or have you?
Best regards, Tim
On 10/12/2014 08:25 PM, Simon Jenni wrote:
Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors are:
Final R-work = 0.3221, R-free = 0.3638
phenix.cc_star agrees:
phenix.cc_star com_001.pdb com_001.mtz \ f_obs_labels="F-obs,SIGF-obs" \ f_model_labels="F-model,PHIF-model" \ unmerged_data="xscale.hkl"
r_work: 0.322 r_free: 0.364
so does phenix.model_vs_data:
phenix.model_vs_data com_001.pdb com_001.mtz
r_work : 0.3221 r_free : 0.3638 sigma_cutoff : None
However, when I calculate the R-factors with sftools, I get a discrepancy between the phenix and sftools results:
sftools << eof read com_001_f_model.mtz Y select col R_FREE_FLAGS > 0 correl col FOBS FMODEL select invert correl col FOBS FMODEL quit Y eof
R-work: 33.6 R-free: 38.1
Does anyone perhaps know what causes this difference?
With best regards, Simon
PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497). No indication for a P21 twin (L-test and refinement in P21 with twin law), not higher symmetry spacegroup I222 (alternating strong and weak reflections are visible in the diffraction patterns, resolved structural differences in the two protomers of the dimer). Two datasets from different beamlines. As might be expected, the R-factors after refinement are unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36 with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between different programs to see how they cope with the unexpected bimodal amplitude distribution.
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A