[phenixbb] omit map with phases

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Sep 14 13:45:01 PDT 2009

Hi Jianghai,
phenix.autobuild will use your phases in your input mtz file, assuming
that they are experimental phases. Only experimental phases should be used
in this case. If you have any other type in your input mtz file, then you
should prevent autobuild from using them by saying:

input_labels="FP SIGFP"

or if you want the free R flags:

input_labels="FP SIGFP None None None None None None FreeR"

or something equivalent.  Note that specifying labels is a little
unpleasant in autobuild: you have to supply None for missing ones. From
the autobuild documentation:


The keywords for labels and anticipated input labels (program labels) are:

input_labels (for data file): FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR_flag
input_refinement_labels: FP SIGFP FreeR_flag
input_map_labels: FP PHIB FOM
input_hires_labels: FP SIGFP FreeR_flag
You can find out all the possible label strings in a data file that you
might use by typing:

phenix.autosol display_labels=w1.mtz  # display all labels for w1.mtz

Let me know if that doesn't answer your question!
All the best,
Tom T

>> Hi,
>> When I am using phenix.autobuild to calculate an SA_omit map, I found
>> out the phenix.autobuild automatically used the phases in my mtz
>> file.  How does phenix.autobuild use the phases? and is it a good idea
>> to use phases in omit map calculation?  and what kind of phases are
>> preferred, experimental phases, phases after density modification, and
>> phases after multi-crystal averaging?
>> Thanks.
>> -- Jianghai
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb

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