[phenixbb] Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor

Pei-Chun Lin pclin at hotmail.com
Wed Oct 13 08:23:31 PDT 2010


Hi, Tom,

In the case of Autobuild (version 1.6.4), does the program automatically generate/extend FreeR_flags to the high resolution?

I have a 3 Ang native sca.file and a 3.5 Ang mtz map solved by MAD, and want to extend to 3 Ang for refinement.
I tried phenix.reflection_file_editor in GUI, and the new merging map looks the same as the original one.
I expect to see a map with higher resolution.

What's the difference of  FreeR_flags generated by these two methods?


PC 


> Date: Wed, 13 Oct 2010 04:34:11 -0600
> From: terwilliger at lanl.gov
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
> 
> Hi PC,
> 
> The two methods will give related but not identical results.
> 
> If you say
> 
> phenix.autobuild data=solve_2.mtz hires_file=w1.sca  seq_file=seq.dat
> 
> then the file AutoBuild_run_1_/expts_fobs_phases_freeR_flags.mtz will
> contain:
> FP SIGFP from w1.sca, converted from intensities to amplitudes.
> PHIB FOM HLA HLB HLC HLD from solve_2.mtz
> FreeR_flags generated by phenix.refine
> 
> If you go to the GUI and use phenix.reflection_file_editor you can get a
> similar result if you select
> 
> "all columns" from w1.sca, and select "edit arrays" and choose "output
> reflections as" amplitudes"
> 
> and you select all the columns from solve_2.mtz EXCEPT FP SIGP
> 
> This will yield:
> 
> F+ SIGF+ F-SIGF-  from w1.sca
> PHIB FOM HLA HLB HLC HLD from solve_2.mtz
> FreeR_flags generated by phenix.refine (not identical to the ones above
> from autobuild)
> 
> In your case as you are supplying anomalous data in w1.sca (I assume) it
> may be easiest to let autobuild do it for you as it will merge the F+ and
> F-  while the reflection file editor won't do that quite as easily.
> 
> All the best,
> Tom T
> 
> 
> >>
> >> Hi,
> >>
> >> If I merge my low resolution mtz file with the high resolution sca file
> with phenix.reflection_file_editor GUI,
> >> is it the same as :
> >>
> >> Merge in hires data
> >>
> >>
> >> phenix.autobuild data=solve_2.mtz hires_file=w1.sca  seq_file=seq.dat
> in Phenix Autobuild?
> >>
> >> PC
> >>  		 	   		  _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>
> 
> 
> 
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