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

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 :

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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),

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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

Hi again Peter, Yes, the AutoMR wizard (any version) will run correctly with input MTZ data that are intensities. However all versions up to now will pass this MTZ file on to AutoBuild without conversion to amplitudes and it will be incorrectly interpreted by AutoBuild. Note that this only applies to MTZ files. Any other source of amplitudes/intensities doesn't cause any problem. If you run from the GUI, you will have the chance to set the correct columns in AutoBuild, if amplitudes are available in your data file. From the command_line, for existing versions, you would need to say when you run AutoMR: input_labels='F SIGF' (or whatever your amplitudes are in this MTZ file) All the best, Tom T there has been a bug in autobuild in which the command 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.)

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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']

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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 >> >> >> _______________________________________________ >> phenixbb mailing list >> [email protected] >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > [email protected] > http://www.phenix-online.org/mailman/listinfo/phenixbb >