Hi phenix.autobuild users, I'm sorry to report a serious bug that I have just noticed that applies to MTZ files for autobuild containing intensities. The problem is fixed now. I'm very sorry about this mistake. All the best, -Tom T THE PROBLEM: In all alpha and beta versions of phenix up to now (up to 1.3b/rc6), there has been a bug in autobuild in which the command phenix.autobuild data.mtz model.pdb will misinterpret intensity data as amplitudes if the input file is an mtz file (for example if the mtz file has IMEAN,SIGIMEAN and F,SIGF). (This can also happen in the GUI version, but you will have been presented on screen 3 with a list of data types (FP SIGFP) and columns from the input data file to match them and it is not so likely that you will have chosen to match FP with IMEAN.) You can tell if this has happened in your case by looking for something like (search for the string "Input labels:"): Input labels: ['IMEAN', 'SIGIMEAN', 'None', 'None', 'None', 'None', 'None', 'None', 'FreeR_flag'] in your log file (where the None's don't matter, just the first 2 column names. The columns in this list should be amplitude-containing columns only. If everything is ok.it should look instead like: Input labels: ['F', 'SIGF', 'None', 'None', 'None', 'None', 'None', 'None', 'None'] THE SOLUTION: In existing versions, the solution to this is to either (1) only have amplitude arrays in your mtz file, or (2) use the GUI and select the correct amplitude arrays, or (3) specify what amplitude columns to use with a command like: input_labels="F SIGF". Note that you cannot use intensity data from an mtz file with the existing versions of autobuild, only amplitude data. In the corrected version (1.3b/rc7, not yet out) , you will be able to use an mtz file with intensity data as long as there is no amplitude data in the same mtz file. Note also that all this applies equally to the refinement_file and hires_file data. Also note that if the file type is not mtz, then this bug does not apply (because the file is always imported and converted from intensities to amplitudes automatically). Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB