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LocScale is a reference-based local amplitude scaling tool using information on expected electron scattering properties of biological macromolecules to improve contrast of cryo-EM density maps.
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To reliably reflect the required level of local sharpening and local resolution variation in the target map, atomic B-factors of the reference model should have been refined using appropriate protocols prior to scaling. It is also possible to use LocScale for local sharpening without a model in cases where an atomic model is not available. The method is described in more detail here [\[1\]](https://doi.org/10.7554/eLife.27131). |
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To reliably reflect the required level of local sharpening and local resolution variation in the target map, atomic B-factors of the reference model should have been refined using appropriate protocols prior to scaling. It is also possible to use LocScale for local sharpening without a model in cases where an atomic model is not available. The method is described in more detail here [\[1\]](https://doi.org/10.7554/eLife.27131).
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## LocScale arguments
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```
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optional arguments:
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-h, --help show this help message and exit
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-em EMMAP_PATH, --emmap_path EMMAP_PATH
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Path to unsharpened EM map
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-hm HALFMAP_PATHS, --halfmap_paths HALFMAP_PATHS
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Paths to first and second halfmaps
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-mm MODEL_MAP, --model_map MODEL_MAP
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Path to model map file
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-mc MODEL_COORDINATES, --model_coordinates MODEL_COORDINATES
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Path to PDB file
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-ma MASK, --mask MASK
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Input filename mask
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-o OUTFILE, --outfile OUTFILE
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Output filename
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-v, --verbose Verbose output
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--output_report Print a PDF copy of the report
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--report_filename REPORT_FILENAME
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Filename for storing PDF output and statistics
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-op OUTPUT_PROCESSING_FILES, --output_processing_files OUTPUT_PROCESSING_FILES
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Path to store processing files
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-wn WINDOW_SIZE, --window_size WINDOW_SIZE
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window size in pixels
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-mpi, --mpi MPI version
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-np NUMBER_PROCESSES, --number_processes NUMBER_PROCESSES
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Number of processes to use
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-ref_it REFMAC_ITERATIONS, --refmac_iterations REFMAC_ITERATIONS
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For atomic model refinement: number of refmac
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iterations
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-res REF_RESOLUTION, --ref_resolution REF_RESOLUTION
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Resolution target for Refmac refinement
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-p APIX, --apix APIX pixel size in Angstrom
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--add_blur ADD_BLUR Globally sharpen the target map for REFMAC refinement
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--refmac5_path REFMAC5_PATH
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Path to refmac5 executable
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-mres MODEL_RESOLUTION, --model_resolution MODEL_RESOLUTION
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Resolution limit for Model Map generation
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-sym SYMMETRY, --symmetry SYMMETRY
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Impose symmetry condition for output
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-fdr_w FDR_WINDOW_SIZE, --fdr_window_size FDR_WINDOW_SIZE
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window size in pixels for FDR thresholding
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-fdr_f FDR_FILTER, --fdr_filter FDR_FILTER
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Pre-filter for FDR thresholding
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-pm PSEUDOMODEL_METHOD, --pseudomodel_method PSEUDOMODEL_METHOD
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For pseudo-atomic model: method
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-pm_it TOTAL_ITERATIONS, --total_iterations TOTAL_ITERATIONS
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For pseudo-atomic model: total iterations
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-dst DISTANCE, --distance DISTANCE
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For pseudo-atomic model: typical distance between
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atoms
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-mw MOLECULAR_WEIGHT, --molecular_weight MOLECULAR_WEIGHT
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Input molecular weight (in kDa)
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--build_ca_only For gradient pseudomodel building: use only Ca atoms
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with interatomic distance 3.8
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-s SMOOTH_FACTOR, --smooth_factor SMOOTH_FACTOR
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Smooth factor for merging profiles
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--boost_secondary_structure BOOST_SECONDARY_STRUCTURE
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Amplify signal corresponding to secondary structures
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--no_reference Run locscale without using any reference information
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--dev_mode If true, this will force locscale to use the
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theoretical profile even if model map present and will
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not check for user input consistency
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--ignore_profiles Ignore average secondary structure profile during
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local scaling
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--skip_refine Ignore REFMAC refinement
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```
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## EMmerNet arguments
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```
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usage: locscale run_emmernet [-h] (-em EMMAP_PATH | -hm HALFMAP_PATHS)
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[-o OUTFILE] [-op OUTPUT_PROCESSING_FILES] [-v]
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[-trained_model {model_based,model_free,ensemble}]
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[-s STRIDE] [-bs BATCH_SIZE]
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[-gpus GPU_IDS [GPU_IDS ...]]
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optional arguments:
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-h, --help show this help message and exit
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-em EMMAP_PATH, --emmap_path EMMAP_PATH
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Path to unsharpened EM map
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-hm HALFMAP_PATHS, --halfmap_paths HALFMAP_PATHS
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Paths to first and second halfmaps
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-o OUTFILE, --outfile OUTFILE
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Output filename
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-op OUTPUT_PROCESSING_FILES, --output_processing_files OUTPUT_PROCESSING_FILES
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Path to store processing files
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-v, --verbose Verbose output
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-trained_model {model_based,model_free,ensemble}, --trained_model {model_based,model_free,ensemble}
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Type of emmernet model to use
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-s STRIDE, --stride STRIDE
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Stride for EMMERNET
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-bs BATCH_SIZE, --batch_size BATCH_SIZE
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Batch size for EMMERNET
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-gpus GPU_IDS [GPU_IDS ...], --gpu_ids GPU_IDS [GPU_IDS ...]
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numbers of the selected GPUs, format: '1 2 3 ... 5'
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``` |
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