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

Tom Terwilliger terwilliger at lanl.gov
Tue Dec 18 15:16:44 PST 2007

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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