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Requires `sparx` , `EMAN2` and `PHENIX`.
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Requires `sparx` , `EMAN2` and `PHENIX`.
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```
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```
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usage: locscale.py -c model.pdb -m map.mrc -dmin resolution
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usage: locscale_v10.py [-h] -em EM_MAP -mm MODEL_MAP -p APIX [-ma MASK]
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[-h] [--out OUT] [--mask MASKFILE]
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[-w WINDOW_SIZE] -o OUTFILE [-mpi]
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[--table TABLE] [--level LEVEL]
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[--radius RADIUS] [--bfactor BFACTOR]
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[--threshold THRESHOLD] [--overall]
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[--verbose]
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*** Performs local amplitude scaling against atomic reference ***
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*** Performs local amplitude scaling against atomic reference ***
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Input:
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Optional arguments:
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-c model.pdb, --model model.pdb
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-h, --help show this help message and exit
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Input filename PDB
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-em EM_MAP, --em_map EM_MAP
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-m map.ccp4, --map map.ccp4
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Input filename EM map
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Input filename map
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-mm MODEL_MAP, --model_map MODEL_MAP
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-dmin resolution map resolution
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Input filename PDB map
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-p APIX, --apix APIX pixel size in Angstrom
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-ma MASK, --mask MASK
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Input filename mask
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-w WINDOW_SIZE, --window_size WINDOW_SIZE
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window size in pixel
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-o OUTFILE, --outfile OUTFILE
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Output filename
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-mpi, --mpi MPI version call by: "mpirun -np 4 python locscale.py
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-em map1.mrc -mm map2.mrc -ma mask.mrc -p 1.0 -w 10
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-mpi -o scaled.mrc"
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Options:
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-h, --help show this help message and exit
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--out OUT Output filename RSCC table
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--mask MASKFILE Input filename mask
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--table TABLE Scattering table [electron, itcc]
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--level LEVEL level of rscc computation [atom, residue, auto]
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--radius RADIUS atom radius [A]
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--bfactor BFACTOR set bfactor [A^2]
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--threshold THRESHOLD only print residues with rscc < threshold
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--overall only prints overall cc
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--verbose print result to stdout
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```
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```
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__* Note:__ Input map needs to be in CCP4 format!
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__* Note:__ Input map needs to be in CCP4/MRC format!
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[source](source) |
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[source](source) |
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