model_map_generation.md

 #### Model 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 and contrast expressed in atomic B-factors. We therefore highly recommend to first perform coordinate and ADP refinement against a globally sharpened and (locally) filtered map as described in our bioRxiv preprint [1].
+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 [1].
 
-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 check consistency with the experimental data using the provided [```prepare_locscale_input.py```](prepare_locscale_input.py) script.  
+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 [```prepare_locscale_input.py```](prepare_locscale_input.py) script.  
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 In the following the procedure is illustrated for TRPV1 channel [2] from the EMDB Model Challenge [3]. All required files can be found [here](http://emsearch.rutgers.edu/atlas/5778_downloads.html).
  
@@ -28,13 +28,13 @@ CCTBX/CCP4 follow the ZXY map axis order convention, whereas most EM programs fo
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-By default structure factors from the model are computed up to the theoretical sampling maximum at Nyquist frequency. This is the preferred procedure for sharpening using LocScale. A different resolution cut-off for computation of the reference map can be supplied using the ```-dmin``` flag, e.g.
+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 parameterized electron scattering factors for neutral atoms. To take into account charged atoms please consult reference [4] and modify the tabulated electron scattering table accordingly.
+Please be aware that CCTBX currently only supports electron scattering factors parameterized for neutral atoms. To take into account atomic charges please consult reference [4] and modify the tabulated electron scattering table accordingly.
 
 See [```prepare_locscale_input.py```](prepare_locscale_input) script for further options.
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