model_map_generation.md

 #### 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.
+Produce 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].
 
 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.  
   <br>
-In the following the procedure is illustrated for TRPV1 channel [1] from the EMDB Model Challenge [2]. All required files can be found [here](http://emsearch.rutgers.edu/atlas/5778_downloads.html).
+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).
  
 ```
 phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
@@ -18,7 +18,8 @@ This procedure generates three files:
 
 <br>
 The two MRC maps are to be used for input in the LocScale procedure.  
-By default structure factors from the model are computed to Nyquist frequency. This is the preferred procedure for LocScale processing.   
+  
+By default structure factors from the model are computed to Nyquist frequency. This is the preferred procedure for sharpening using LocScale.   
 A different resolution cut-off can be supplied using the ```-dmin``` flag. See 
 
 ```
@@ -27,12 +28,13 @@ phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -d
   
 See [```prepare_locscale_input.py```](prepare_locscale_input.py) script for further options.
 <br>  
-LocScale maps can be computed using any source of reference maps for scaling. If you prefer to use your own procedure to generate reference model maps, we do recommend to make sure your map complies with the [following procedure](model_map_generation_from_arbitrary_files).    
+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](model_map_generation_from_arbitrary_files).    
 
 #### Link to [source](https://git.embl.de/jakobi/LocScale/blob/master/prepare_locscale_input.py)  
 
 [//]: # (#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__)
 
 References:  
-[[1]](https://www.nature.com/nature/journal/v504/n7478/full/nature12822.html) Liao et al., _Nature_ __504__:107-112 (2013)   
-[[2]](http://challenges.emdatabank.org/?q=model_challenge) EMDB Model Challenge 2015/2016
+[[1]](https://doi.org/10.1101/121913) Jakobi et al. bioRxiv 121913; [doi: https://doi.org/10.1101/121913](doi: https://doi.org/10.1101/121913) (2017)  
+[[2]](https://www.nature.com/nature/journal/v504/n7478/full/nature12822.html) Liao et al., _Nature_ __504__:107-112 (2013)   
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+[[3]](http://challenges.emdatabank.org/?q=model_challenge) EMDB Model Challenge 2015/2016
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