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

[Thomas C. Terwilliger]

Hi Peter,
That one should take intensities just fine. There is an explicit step to
convert intensities to amplitudes in the wizard.  I will have to check
however as to whether an MTZ file with intensities will have been passed
on to the AutoBuild wizard correctly...
-Tom T

> Hi Tom,
>
> What about the AutoMR wizard. Can I use intensities there instead of
> amplitudes? I always get confused.
>
> Thanks,
>
> Peter
>
> 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
>>
>>
>> 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: 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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