Hi Wojtek, you need to convert your EM map into a reflection file (for example, cns or mtz formatted, format doesn't matter). This reflection file should contain "Fobs" - the amplitudes of Fourier map coefficients and phases corresponding to your EM map. The phases should be presented as Hendrickson-Lattmann coefficients (in this case only A and B will be non-zero, and C=D=0). Them phenix.refine should deal with this all right.
I think the problem you face stems from the fact that when you convert your EM map into a reflection file the "Fobs" you get are complex values (or pairs: amplitude Fobs and phase PHobs), which phenix.refine would not take as observations. If you send me the file (off-list !) I may offer more comments. Pavel On Fri, Jul 13, 2012 at 8:28 AM, Wojtek Potrzebowski <wpotr...@genesilico.pl > wrote: > Dear all, > I want to refine a model of the complex that consists of rigid subunits > using an electron microscopy electron density map. > I've tried to use phenix for this purpose. Thus I have to back-FT the > electron density map to a mtz reflection file. > I've experienced problem using sfall for this purpose, but cinvfft has > done a job (I can read a resulting file with mtzdmp). > However phenix doesn't read this file properly (data labels box is empty). > Can anyone help me on this, please? > I am looking forward to hearing from you, > Wojtek >
