Reference map generation from a PDB coordinate model
Producing locally contrast-optimized maps using LocScale requires a reference model map that accurately reflects the variation in resolution expressed in atomic B-factors. We therefore recommend to first perform coordinate and ADP refinement against a globally sharpened and (locally) filtered map as described the 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 map and to check consistency with the experimental data using the provided
In the following the procedure is illustrated for TRPV1 channel  from the EMDB Model Challenge . All required files can be found here.
phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -ma emd_5778_mask.map
This procedure generates four files:
pdb3j5p_4locscale.pdb(shifted) PDB model with same P1 unit cell as EM map
pdb3j5p_4locscale.mrc(shifted) reference model map
emd_5778_full_4locscale.mrc(shifted) original reconstruction
The two MRC maps produced (`pdb3j5p_4locscale.mrc` and `emd_5778_full_4locscale.mrc`) along with the mask (`emd_5778_mask_4locscale.mrc`) are to be used for input in the LocScale procedure.
CCTBX/CCP4 follow the ZXY map axis order convention, whereas most EM programs follow XYZ. This will mostly not have any consequences for visualization, but it may cause issues in further processing (i.e. result in inverted hand of the output maps).
here.It is preferable to proceed in XYZ convention, please see
By default structure factors from the model are computed up to the theoretical sampling maximum at Nyquist frequency. A different resolution cut-off for computation of the reference map can be supplied using the ```-dmin``` flag, e.g.
phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -ma emd_5778_mask.map -dmin 4.0
Please be aware that CCTBX currently only supports electron scattering factors parameterized for neutral atoms. To take into account atomic charges please consult reference  and modify the tabulated electron scattering table accordingly.
prepare_locscale_input.py script for further options.
LocScale maps can be computed using any source of reference maps for scaling. If you prefer to use your own workflow to generate reference model maps, we do recommend to make sure your map complies with the following procedure.
[//]: # (#### PLEASE download the following electron form factor table for use with pdb2map.py.)