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
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