brr.... at the moment, the maps are indeed not on absolute scale, will change that.
P 2008/10/10 Paul Emsley <[EMAIL PROTECTED]>: > Lieven Buts wrote: >> >> Hello all, >> >> I have just been experimenting with the refinement options for twinned >> data >> in phenix.refine (final 1.3 version), and I ran into a strange problem >> with >> the density fit validation function in Coot 0.4 and 0.5. When I >> "auto-open" >> the MTZ file with map coefficients produced by phenix.refine, I get a >> normal-looking map, but every single residue in the density fit plot is >> squarely in the red. When I open the 2Fo-Fc CNS format file also produced >> by phenix.refine, I get a map that looks identical to the first one, and >> when I validate the same model against the new map, I get the normal >> density fit pattern, with most residues in the green, and the occasional >> orange one. So it seems that the density fit calculation goes wrong for >> MTZ files from twinned refinement. Does anyone know what might be >> causing this? I can send the data files if required. > > > Randy Read told me about this issue the other day. > > The density fit graphs work assuming that the map is on the absolute scale - > I suspect that your maps have a different scale (test by looking at the > absolute level given the same number of sigma). It would be better if Coot > used correlation vs a calculated map, but today it does not. > > You can adjust the scale using Extensions -> Refine -> Set Density Fit Graph > Weight [1] > > [1] I may move this soon - Settings would seem a better submenu. > > Paul. > -- ----------------------------------------------------------------- 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 -----------------------------------------------------------------
