phenix.refine also might not (by default) use missing data in map calculation. AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe this changed now). When your high resolution shells are incomplete (like when using the anisotropy server to perform elliptical data truncation, or etc etc), I can imagine that the use of DFc can have considerable effect on the looks of a map.
P 2008/9/28 Kevin Cowtan <[EMAIL PROTECTED]>: > Another factor may be that phenix.refine does not make a full use of > experimental phase information in its calculation of the error parameters - > I've been discussing this with Peter, Randy and Ralph. I don't know that > this is the cause, but I see inferior results when recycling buccaneer with > phenix.refine (although this is confounded by the fact that phenix.refine > doesn't output the updated ABCD's. Having said that, neither does refmac, > but it does give me something I can fudge. Both Garib and Pavel could toss > me a bone here). > > A corollary is that phenix.refine may also not use the experimental phase > information in its map coefficients - I simply assumed that it did, but that > assumption may be unwarranted. > > Both of these factors would affect the quality of the maps when refining > with experimental phasing (assuming a good modern phasing program). However > if the difference is also present after MR, then you need to look elsewhere > for an explanation. > > Kevin > > Dunten, Pete W. wrote: >> >> >> I mentioned previously phenix.refine tosses your weak data if IMEAN, >> SIGIMEAN are chosen during refinement. >> >> >> I'm wondering if this omission of weak Fobs from the Fobs-Fcalc difference >> map explains why the difference maps out of refmac seem to be more helpful >> in showing where to move atoms. >> >> D. Crowfoot et al. in The Chemistry of Penicillin (1949) explain why this >> might be so, and Stout & Jenson elaborate the argument. Briefly, the >> calculated phase will be closest to the phase of the vector difference Fcalc >> – Fobs when |Fcalc| > |Fobs|. >> >> I leave it to the reader to try calculating some maps with and without the >> weak Fobs in phenix.refine or refmac, and perhaps making some deliberate >> rotamer errors, to see if using the complete data with weak Fobs helps. >> > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------
