#### Model map generation from a PDB coordinate model
To produce the desired result of locally contrast-optimized maps, LocScale requires a reference model map that accurately reflects the variation in resolution and contrast expressed in atomic B-factors. We therefore highly recommend to first perform coordinate refinement against a globally sharpened and locally filtered map as described in our BioRxiv preprint.
The model map can be generated by any procedure that computes the model map from B-factor weighted structure factors using electron scattering atomic form factors. We here provide a recommended procedure to generate the model maps:
__Note that normally steps 1-3 are not required if model and map have already been refined__
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__(1)__ The EM map should be zero-based, i.e. the map origin should be located at (0,0,0). The [```check_and_set_ori_zero.py```](check_and_set_ori_zero) script is a quick way to ascertain the map is zero-based.
__(2)__ If the map was already zero-based this step can be skipped. If the map was shifted in (1), the PDB model should be shifted by the same amount in real coordinates (i.e. voxel_shift*pixel_size).
- Open model and map in Chimera (```chimera em_map.mrc pdb_model.pdb &```)
- Shift model to fit with zero-based map (```move -45 -45 -45 model #1 coord #1```)
- Save model relative to map coordinates (```write format pdb relative #1 #0 filename.pdb```)
__(3)__ Check if PDB symmetry matches that of EM map.
To generate a model map with B-facvtor weighted structure factors and electron form factors we recommend to use the provided [```pdb2map.py```](pdb2map.pyc) script.
