Main Command Line Programs¶
auto.process¶
Automatically Process a dataset
usage: auto.process [-h] [-m] [-s] [-a] [-b] [-p PREFIX] [-d DIR] [-z] [-l] [-x] [--formula FORMULA] [images ...]
Positional Arguments¶
- images
Data sets to process. Each data set can be represented by any frame from that set. If no datasets are provided, attempt to resume from a previous checkpoint file
Named Arguments¶
- -m, --mad
Process each set, scale together and generate separate outputs.
Default: False
- -s, --screen
Process a few frames to characterize crystal
Default: False
- -a, --anom
Process with Friedel’s law False
Default: False
- -b, --backup
Backup existing directory
Default: False
- -p, --prefix
comma separated list of prefixes to use for output files
- -d, --dir
Directory to store output files. If not provided a new one is created
- -z, --zap
Abandon saved state and start all over. Must be in a results directory.
Default: False
- -l, --load
Load manually processed dataset
Default: False
- -x, --nonchiral
Non-chiral spacegroups. Default assumes only chiral molecules
Default: False
- --formula
Solve small molecule with provided formula. Eg Mg1O6H12
Data sets:
Each data set can be represented by any frame from that set. If multiple frames are provided but no MAD modifier options (-m, –mad) is provided, each set will be processed, and at the end all the datasets will be scaled together and merge into a single output reflection file.
Examples:
- auto.process –mad /path/to/dataset_{peak,infl,remo}_001.img
process a 3-dataset MAD
- auto.process /path/to/dataset_{hires,lores}_001.img
process and merge low-resolution and hi-resolution datasets
- auto.process /path/to/dataset_hires_001.img /path/to/dataset_lores_001.img
process and merge low-resolution and hi-resolution datasets. Same as above.
- auto.process –screen /foo/bar/test_001.img –dir /foo/screen_output
Screen dataset and place the output in the given directory
auto.integrate¶
Resume/repeat/optimize a previous processing from the integration step
usage: auto.integrate [-h] [-a] [-b] [-f FRAMES] [-x EXCLUDE] [-d DIR] [-o] [-r RES]
Named Arguments¶
- -a, --anom
Process with Friedel’s law False
Default: False
- -b, --backup
Backup existing directory
Default: False
- -f, --frames
Data range e.g. <start>-<end>
- -x, --exclude
Exclude frame ranges e.g. <start>-<end>,<start>-<end>,…
- -d, --dir
Directory containing previous processing. Default is current directory.
- -o, --opt
Optimize integration using refined parameters from previous run.
Default: False
- -r, --res
Force high resolution limit
Examples:
- auto.integrate -r 2.2 -f 5-180 -o
Optimize the integration, restring to resolution 2.2, and only process frames 5 to 180
- auto.integrate –frames 20-120 –exclude 1-2,310-220 –anom
Repeat the integration considering only frames 20 to 120 with Friedel’s law False for all remainig steps. Also skip frames 1-2 and 310-220
auto.scale¶
Resume/repeat/optimize a previous processing from the scaling step
usage: auto.scale [-h] [-a] [-b] [-d DIR] [-r RES]
Named Arguments¶
- -a, --anom
Process with Friedel’s law False
Default: False
- -b, --backup
Backup existing directory
Default: False
- -d, --dir
Directory containing previous processing. Default is current directory.
- -r, --res
Force high resolution limit
Examples:
- auto.scale -r 2.0
scale with high-resolution limit of 2.0 A
- auto.scale –anom
scale with Friedel’s law False
auto.strategy¶
Resume/repeat a previous screening from the strategy step
usage: auto.strategy [-h] [-a] [-b] [-d DIR] [-r RES]
Named Arguments¶
- -a, --anom
Process with Friedel’s law False
Default: False
- -b, --backup
Backup existing directory
Default: False
- -d, --dir
Directory containing previous processing. Default is current directory.
- -r, --res
Force high resolution limit
auto.symmetry¶
Resume/repeat/optimize a previous processing from the scaling step
usage: auto.symmetry [-h] [-a] [-b] [-d DIR] [-r RES] [-g SPACEGROUP] [-x]
Named Arguments¶
- -a, --anom
Process with Friedel’s law False
Default: False
- -b, --backup
Backup existing directory
Default: False
- -d, --dir
Directory containing previous processing. Default is current directory.
- -r, --res
Force high resolution limit
- -g, --spacegroup
Manually set space group by number
- -x, --nonchiral
Non-chiral spacegroups. Default assumes only chiral molecules
Default: False
Space group numbers for Bravais lattice types:
- aP
P1(#1)
- mP
P2(#3), P2₁(#4)
- mC
C2(#5)
- oP
P222(#16), P222₁(#17), P2₁2₁2(#18), P2₁2₁2₁(#19)
- oC
C222₁(#20), C222(#21)
- oF
F222(#22)
- oI
I222(#23), I2₁2₁2₁(#24)
- tP
P4(#75), P4₁(#76), P4₂(#77), P4₃(#78), P422(#89) P42₁2(#90), P4₁22(#91), P4₁2₁2(#92), P4₂22(#93), P4₂2₁2(#94) P4₃22(#95), P4₃2₁2(#96)
- tI
I4(#79), I4₁(#80), I422(#97), I4₁22(#98)
- hP
P3(#143), P3₁(#144), P3₂(#145), P312(#149), P321(#150) P3₁12(#151), P3₁21(#152), P3₂12(#153), P3₂21(#154), P6(#168) P6₁(#169), P6₅(#170), P6₂(#171), P6₄(#172), P6₃(#173) P622(#177), P6₁22(#178), P6₅22(#179), P6₂22(#180), P6₄22(#181) P6₃22(#182)
- hR
R3(#146), R32(#155)
- cP
P23(#195), P2₁3(#198), P432(#207), P4₂32(#208), P4₃32(#212) P4₁32(#213)
- cF
F23(#196), F432(#209), F4₁32(#210)
- cI
I23(#197), I2₁3(#199), I432(#211), I4₁32(#214)