harpcalc

harpcalc is a command line interface (CLI) to performing HARP calculations.

Usage

Usage:

harpcalc [-h] (-f F F | -id ID) [--authid] [-o  OUTPUT] [--label_sf LABEL_SF] [--label_phase LABEL_PHASE] [--atoms_min ATOMS_MIN] [--atoms_max ATOMS_MAX] [--atoms_num ATOMS_NUM] [--voxel_offset VOXEL_OFFSET] [--blobs_min BLOBS_MIN] [--blobs_max BLOBS_MAX] [--blobs_num BLOBS_NUM] [--skip_calc] [--skip_load] [--only_polymers] [--output_bfactor] [--remove_metals] [--remove_water] [--verbose | --quiet | --normal] [--use_c | --use_python] [-c CHAINS [CHAINS ...]]

Use HARP to evaluate the atomic resolution and map-to-model agreement for a molecular model.

Options:

Tag	Descrption
-h, --help	Show this help message and exit
-f F F	Location of mmcif file and density file
-id ID	The ID of the structure in the wwPDB to process
--authid	Use Auth ID instead of Label ID
-o OUTPUT, --output OUTPUT	Directory to store results and files
--label_sf LABEL_SF	Structure factor label in X-ray file
--label_phase LABEL_PHASE	Phase label in X-ray file
--atoms_min ATOMS_MIN	Minimum width of atoms to check (standard deviation of 3D normal distribution)
--atoms_max ATOMS_MAX	Maximum width of atoms to check (standard deviation of 3D normal distribution)
--atoms_num ATOMS_NUM	Number of atoms models to use. Spaced evenly in log-space between atom_min and atom_max
--voxel_offset VOXEL_OFFSET	Cartesian coordinate offset for each density voxel to relate to atomic model coordinates. A value of 0.0 is edge centered, 0.5 is face centered.
--blobs_min BLOBS_MIN	Minimum width of a blob to check (standard deviation of 3D normal distribution)
--blobs_max BLOBS_MAX	Maximum width of a blob to check (standard deviation of 3D normal distribution)
--blobs_num BLOBS_NUM	Number of blobs to use. Spaced evenly between blob_min and blob_max
--skip_calc	Skip the HARP calculation, still download and visualize
--skip_load	Skip loading molecule and density
--only_polymers	Only run HARP calculations for chains that come from entities that are polymers
--output_bfactor	Output a version of the structure with bfactors overwritten with HARP probabilities
--remove_metals	Remove common metal/salt ions from molecule before calculation
--remove_water	Remove waters from molecule before calculation
--verbose
--quiet
--normal
--use_c	Use the C library to render models
--use_python	Use Python to render models
-c CHAINS [CHAINS ...], --chains CHAINS [CHAINS ...]	Chains in mmcif to run the calculation for. Separate by spaces. If not provided, all chains are used.