Curious, will either of the utilities (iotbx.reflection_file_editor or iotbx.r_free_flags_completion_simple) follow --use-lattice-symmetry-in- r-free-flag-generation that phenix.reflection_file_converter offers? Thanks F On May 19, 2010, at 10:20 AM, Tom Terwilliger wrote:
Hi Robert, You can do this really easily in the PHENIX GUI with the reflection file editor. If you want to use a command-line tool you can also use iotbx.r_free_flags_completion_simple. All the best, Tom T
On May 19, 2010, at 10:18 AM, David Cobessi wrote:
Hi Robert, Using CCP4... ;-) (maybe Freerflag) you can do it.... David
Robert Immormino wrote:
Hi,
Hopefully I'm just missing something obvious....
I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution.
I've tried:
phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz
and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both.
I also tried with phenix.refine
phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags"
This seems closer, but I get the error:
Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement:
Thanks, -bob _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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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 CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss
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