Map utilities

Making difference maps

rs.internal_diffmap

Make an internal difference map using the given symmetry operation

usage: rs.internal_diffmap [-h] -i mtz data_col sig_col -r ref phi_col -op
                           SYMOP [-a ALPHA] [-d DMAX] [-sg SPACEGROUP]
                           [-o OUTFILE]

-h, --help: show this help message and exit

-i <mtz> <data_col> <sig_col>, --inputmtz <mtz> <data_col> <sig_col>: MTZ to be used for internal difference map. Specified as (filename, F, SigF)

-r <ref> <phi_col>, --refmtz <ref> <phi_col>: MTZ containing isomorphous phases to be used. Specified as (filename, Phi).

-op <symop>, --symop <symop>: Symmetry operation to use to compute internal difference map. Can be given as ISYM if used with a spacegroup argument.

-a <alpha>, --alpha <alpha>: alpha value for computing difference map weights (default=0.0)

-d <dmax>, --dmax <dmax>: If set, dmax to truncate difference map

-sg <spacegroup>, --spacegroup <spacegroup>: Spacegroup to use for symmetry operation (only necessary if op specifies an ISYM).

-o <outfile>, --outfile <outfile>: Output MTZ filename

rs.diffmap

Make an ordinary difference map between columns of data.

The naming convention chosen for inputs is on and off, such that the generated differrence map will be |F_on| - |F_off|.

usage: rs.diffmap [-h] -on mtz data_col sig_col -off mtz data_col sig_col -r
                  ref phi_col [-a ALPHA] [-d DMAX] [-o OUTFILE]

-h, --help: show this help message and exit

-on <mtz> <data_col> <sig_col>, --onmtz <mtz> <data_col> <sig_col>: MTZ to be used as on data. Specified as (filename, F, SigF)

-off <mtz> <data_col> <sig_col>, --offmtz <mtz> <data_col> <sig_col>: MTZ to be used as off data. Specified as (filename, F, SigF)

-r <ref> <phi_col>, --refmtz <ref> <phi_col>: MTZ containing isomorphous phases to be used. Specified as (filename, Phi).

-a <alpha>, --alpha <alpha>: alpha value for computing difference map weights (default=0.0)

-d <dmax>, --dmax <dmax>: If set, dmax to truncate difference map

-o <outfile>, --outfile <outfile>: Output MTZ filename

Finding map peaks

rs.find_peaks

Search an electron density map for peaks in the vicinity of a structure.

usage: rs.find_peaks [-h] -f STRUCTURE_FACTOR_KEY -p PHASE_KEY [-o CSV_OUT]
                     [-z SIGMA_CUTOFF] [-w WEIGHT_KEY]
                     [--sample-rate SAMPLE_RATE] [--min-volume MIN_VOLUME]
                     [--min-score MIN_SCORE] [--min-peak MIN_PEAK]
                     [-d DISTANCE_CUTOFF] [--use-long-names]
                     mtz_file pdb_file

mtz_file

pdb_file

-h, --help: show this help message and exit

-f <structure_factor_key>, --structure-factor-key <structure_factor_key>: column label of the structure factor you want to use.

-p <phase_key>, --phase-key <phase_key>: column label of the phase you want to use.

-o <csv_out>, --csv-out <csv_out>: output the report to a csv file

-z <sigma_cutoff>, --sigma-cutoff <sigma_cutoff>: the z-score cutoff for voxels to be included in the peak search. the default is 1.5

-w <weight_key>, --weight-key <weight_key>: column label of any weights you wish to apply to the map.

--sample-rate <sample_rate>: change fft oversampling from the default (3).

--min-volume <min_volume>: the minimum volume of peaks with default zero.

--min-score <min_score>: the minimum score of peaks with default zero.

--min-peak <min_peak>: the minimum peak value with default zero.

-d <distance_cutoff>, --distance-cutoff <distance_cutoff>: the distance cutoff of nearest neighbor search with default of 4 angstroms.

--use-long-names: use more verbose column names in the peak report.

rs.find_difference_peaks

Search an electron density map for peaks in the vicinity of a structure.

usage: rs.find_difference_peaks [-h] -f STRUCTURE_FACTOR_KEY -p PHASE_KEY
                                [-o CSV_OUT] [-z SIGMA_CUTOFF] [-w WEIGHT_KEY]
                                [--sample-rate SAMPLE_RATE]
                                [--min-volume MIN_VOLUME]
                                [--min-score MIN_SCORE] [--min-peak MIN_PEAK]
                                [-d DISTANCE_CUTOFF] [--use-long-names]
                                mtz_file pdb_file

mtz_file

pdb_file

-h, --help: show this help message and exit

-f <structure_factor_key>, --structure-factor-key <structure_factor_key>: column label of the structure factor you want to use.

-p <phase_key>, --phase-key <phase_key>: column label of the phase you want to use.

-o <csv_out>, --csv-out <csv_out>: output the report to a csv file

-z <sigma_cutoff>, --sigma-cutoff <sigma_cutoff>: the z-score cutoff for voxels to be included in the peak search. the default is 1.5

-w <weight_key>, --weight-key <weight_key>: column label of any weights you wish to apply to the map.

--sample-rate <sample_rate>: change fft oversampling from the default (3).

--min-volume <min_volume>: the minimum volume of peaks with default zero.

--min-score <min_score>: the minimum score of peaks with default zero.

--min-peak <min_peak>: the minimum peak value with default zero.

-d <distance_cutoff>, --distance-cutoff <distance_cutoff>: the distance cutoff of nearest neighbor search with default of 4 angstroms.

--use-long-names: use more verbose column names in the peak report.