Hi PC,
Hi,
I know this topic was discussed before, but I am still confused and still unable to refine my map merged from hires data because phenix.refine complains "No array of R-free flags found"
The command was used to generate a hires map. phenix.autobuild data=resolve_1.mtz hires_file=hires.sca \seq_file=sequence.dat maps_only=True
So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild folder,
What this command has done is to take the phases in resolve_1.mtz and combined them with amplitudes from hires.sca and added free R flags to generate exptl_fobs_phases_freeR_flags.mtz . Additionally the file overall_best_denmod_map_coeffs.mtz now contains the above amplitudes along with some kind of density-modified phases. I would caution that this is probably not what you really wanted to do. Instead: Almost always you should use for "data=" a file that contains experimental phases only (not density-modified phases). So it would be better to use the command: phenix.autobuild data=phaser_1.mtz hires_file=hires.sca \ eq_file=sequence.dat maps_only=True which would instead density modify using hl coeffs from modify phaser_1.mtz, extending phase information to the data in hires.sca . Now you will have exptl_fobs_phases_freeR_flags.mtz with (a) experimental amplitudes from hires.sca (b) experimental phases and hl coefficients (where available) from phaser_1.mtz (c) free R flags to the full resolution of hires.sca and overall_best_denmod_map_coeffs.mtz with coefficients for a density-modified map at the resolution of hires.sca.
How do I merge low and high resolution data by "phenix.reflection_file_editor"? What files (input and output arrays) should I choose?
I think reflection_file_editor will only copy arrays (or columns) of data,
and not merge several columns of data into one. Note that merging high
and low resolution data requires (1) a scale factor between the datasets
and (2) possibly a b-factor or anisotropic b-factor relating the two
datasets. It cannot be properly done simply by merging reflection files.
The reflection_flle_editor will add free R flags if they are missing or
extend them for you if they are present only to low resolution, however.
This allows you to take a low-res dataset with free R flags and a high-res
dataset with no free R and to transfer the existing low-res free R flags
to the high-res dataset and to extend them to full resolution.
If you want, you can use phenix.solve to scale low and high resolution
data by pretending that they are part of a mad dataset:
make a file "scale.csh" like this, after editing to match your case:
#!/bin/csh -f
cp $PHENIX/solve_resolve/ext_ref_files/c2.sym .
phenix.solve<