LocScale performs local amplitude scaling based on a atomic reference structure.
LocScale uses rotationally averaged reference amplitudes from a refined atomic model to locally scale (sharpen) amplitudes of the Fourier transform of a cryo-EM potential map, keeping the phases constant.
For sharpening LocScale requires the unfiltered, unsharpened EM reconstruction (or half maps) along with a reference map computed from the atomic model. Optionally, a mask may be applied to speed up the computation.
Please follow these instructions to generate your model-based reference map with B-factor weighted structure factors using electron form factors.
Invoking locscale_mpi.py: The script needs to be invoked within the EMAN2/Sparx Python framework, i.e. if EMAN2 Python is the default Python framework:
python locscale_mpi.py [arguments]
Window size: We find that a window size of approximately (7 * average_map_resolution_in_Å)/pixel_size typically works well.
Computing time: We strongly recommend to run the parallelized version of LocScale using MPI. Computing LocScale maps on a a single node can be (very) slow. In comparison, computation of a LocScale map for EMD-5778 takes about 4 min on 50 CPUs using MPI.