Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
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
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Wed, Oct 13, 2010 at 11:34 AM, Thomas C. Terwilliger
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
Small correction: you need to set these column labels manually - it will by default use I+ SIGI+ I- SIGI-, but this will raise an error if you are converting to amplitudes. I can change the program behavior to do this automatically, but it is potentially dangerous (or at least annoying) if this is done *too* automatically. -Nat
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: [email protected] To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Nathaniel Echols -
Pei-Chun Lin -
Thomas C. Terwilliger