Dear Wojtek, sounds like an mtz format issue. Can you read it in with coot? Maybe Pavel or others have an idea?
Bruno -----Message d'origine----- De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Wojtek Potrzebowski Envoyé : Friday, July 13, 2012 6:51 PM À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] Rigid body refinement with phenix using EM maps. Dear Bruno, Thank you very much for your quick response! I've managed to generate mtz file (I've only needed to add "set spacegroup P1" while running sftools). However, the problem remains. I am not sure if this is the case but Phenix reads columns 1 and 2 as "Map coefs". Do you have any clue? Best regards, Wojtek On 07/13/2012 05:53 PM, Bruno KLAHOLZ wrote: > Dear Wojtek, > > you can try something of this type to get the EM map converted into an hkl > list and mtz file with I's and some sigma I's estimated to 1/10 of the I's > (the latter is required for running fittings/refinements etc.). > > Best, > > Bruno > > > > /usr/local/rave/rave_linux/lx_mapman<<EOF > re m2 name_40-8A.ccp4 ccp4 > no m2 > uvw > m2 > 3 > 1 > 2 > write m2 name_40-8A-uvw.ccp4 ccp4 > quit > EOF > > /usr/local/ccp4-version/bin/sftools<<EOF > MAPIN name_40-8A-uvw.ccp4 map > MAP2SF > calc q col sigma = col 1 10 / > CALC I col test = rfree(0.05) > WRITE name_40-8A-uvw.fobs col 1 3 2 4 > xpl > FOBS > PHASE > write > name_40-8A-uvw.mtz > quit > > > > > -----Message d'origine----- > De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de > Wojtek Potrzebowski Envoyé : Friday, July 13, 2012 5:28 PM À : > CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Rigid body refinement with > phenix using EM maps. > > 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 > > ###################################################################### > ##### > Dr. Bruno P. Klaholz > Department of Integrated Structural Biology Institute of Genetics and > of Molecular and Cellular Biology IGBMC - UMR 7104 - U 964 1, rue > Laurent Fries BP 10142 > 67404 ILLKIRCH CEDEX > FRANCE > http://www.igbmc.fr/ > http://igbmc.fr/Klaholz > > > >
