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FYI, I just used a Matrix Weight of 2.0e-5, yes that's a weight of 0.00002, on a rather poor 2.9A map generated from a PHS file (XtalView format text filecreated from the CNS omitmap.coeff map output). I have not noted any real problems with REFMAC generated MTZ files, so the weighting must be optimized for REFMAC generated maps. Mark On Thu, 2010-02-04 at 06:22 -0600, Paul Emsley wrote: > Miguel Ortiz Lombardia wrote: > > Le 4 févr. 2010 à 04:37, Norman Zhu a écrit : > > > > > >> hello there > >> > >> I am in the process of refining a protein structure complexed to DNA > >> promoter site. I ran into difficulty as i try to move a few bases into > >> patch of electron density that is obviously meant for them. dragging the > >> bases with real space refine zone and/or regularize zone neither break open > >> the phosphate back bone bounds or turn everything into knots. > >> I know there is nothing wrong with the naming convention of my bases > >> since I changed them from DT to Td after similar blog. > >> Any suggestion on this matter would be greatly appreciated. > >> > >> Norm > >> > >> > > > > Hi Norm, > > > > Depending on the resolution of your data you may need to turn down the matrix weight in refinement parameters. I tipically put this down to 30 (compared to the default value of 60) and for really lower resolution (say 3 or worse) I may go as down as 20. > > > > > > I frequently use 6.0 or even 2.0 sometimes. > > Paul Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto:[log in to unmask] http://xray.utmb.edu http://xray.utmb.edu/~white