Hi Bill, I suspect that the maps in 1.3-rc6 do not use DFc for missing reflections, whereas in 1.4 they do by default. However, in version 1.4 you can make non-filled maps in Coot using the other arrays in the map coefficient file. Could you try this to see if using the unfilled data makes your maps look more like the ones from 1.3b? This would be very interesting to us as we are still trying to assess the impact of filling in missing data. In addition, if you are using experimental phases in the refinement these will be used to make a phase combined map by default. Cheers, Paul On Aug 6, 2009, at 7:43 AM, William G. Scott wrote:
Hi folks:
About a year ago I refined a 1.6 Å RNA structure with phenix.refine 1.3b-rc6 and then got distracted. I picked it up today and essentially repeated the last round of refinement with 1.4-57 (and also 1.4-159). The maps are subtly different, but consistently slightly worse with 1.4.
Here are two examples: http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf
In the second example, this would lead to deletion of one of the octahedrally coordinated waters on a known Mg++ ion.
2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of Mg ++. A similar thing happens with the corresponding water in that structure.
Has the weighting for the bulk solvent mask or something like that been increased?
Thanks.
Bill Scott
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ [email protected] ] [ 1-510-486-7963 ] --