model_map_generation.md

@@ -10,13 +10,14 @@ In the following the procedure is illustrated for TRPV1 channel [1] from the EMD
 phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
 ```
   
-##### This procedure generates three files:  
+This procedure generates three files:  
   
 - pdb3j5p_4locscale.pdb                     (shifted) PDB model with same P1 unit cell as map 
-- `pdb3j5p_4locscale.mrc`                 Reference model map
-- `emd_5778_full_4locscale.mrc`      (shifted) original reconstruction
+- `pdb3j5p_4locscale.mrc`                 __Reference model map__
+- `emd_5778_full_4locscale.mrc`      __(shifted) original reconstruction__
 
 <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.   
 A different resolution cut-off can be supplied using the ```-dmin``` flag. See 
 
@@ -32,6 +33,6 @@ LocScale maps can be computed using any source of reference maps for scaling. If
 
 [//]: # (#### __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
\ No newline at end of file