locscale.protocols.protocol_locscale module

class locscale.protocols.protocol_locscale.ProtLocScale(**kwargs)

Bases: pwem.protocols.protocol_3d.Prot3D

This protocol computes contrast-enhanced cryo-EM maps by local amplitude scaling using a reference model.

convertStep()

createOutputStep()

Create the output volume

getOutputFn()

Returns the scaled output file name.

getSampling()

prepareParams()

The input params of the program are as follows (from source): ‘-em’, ‘–em_map’, required=True, help=’Input filename EM map’) ‘-mm’, ‘–model_map’, required=True, help=’Input filename PDB map’) ‘-p’, ‘–apix’, type=float, required=True, help=’pixel size in Angstrom’) ‘-ma’, ‘–mask’, help=’Input filename mask’) ‘-w’, ‘–window_size’, type=int, help=’window size in pixel’) ‘-o’, ‘–outfile’, required=True, help=’Output filename’) ‘-mpi’, ‘–mpi’, action=’store_true’, default=False,

help=’MPI version call by: “{0}”’.format(mpi_cmd)

refineStep()

Run the LocScale program (with EMAN enviroment) to refine a volume.