[phenixbb] MTZ intensities interpreted as amplitudes by autobuild command-line versions up to 1.3b/rc6

Peter Zwart PHZwart at lbl.gov
Tue Dec 18 15:22:02 PST 2007

Hi Tom,

What about the AutoMR wizard. Can I use intensities there instead of
amplitudes? I always get confused.



2007/12/18, Tom Terwilliger <terwilliger at lanl.gov>:
> 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
> 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']
> 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: terwilliger at LANL.gov
> 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
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