model_map_generation.md

@@ -2,23 +2,29 @@
 
 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 map and check consistency with the experimental data:  
-  
-To generate a model map with B-facvtor weighted structure factors and electron form factors we recommend to use the provided [```prepare_locscale_input.py```](prepare_locscale_input.py) script.
-  
-
-In the following the procedure is illustrated for TRPV1 channel [1]. The files can be found [here](http://emsearch.rutgers.edu/atlas/5778_downloads.html)
+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).
  
 ```
 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` &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  (shifted) PDB model with same P1 unit cell as map 
+- pdb3j5p_4locscale.pdb &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  (shifted) PDB model with same P1 unit cell as map 
 - `pdb3j5p_4locscale.mrc` &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Reference model map
 - `emd_5778_full_4locscale.mrc` &nbsp;&nbsp;&nbsp;&nbsp; (shifted) original reconstruction
 
+<br>
+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 
+
+```
+phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -dmin 4.0
+```  
+  
+See [```prepare_locscale_input.py```](prepare_locscale_input.py) script for further options.
   
 #### Link to [source](https://git.embl.de/jakobi/LocScale/blob/master/prepare_locscale_input.py)  
 [recommended procedure](model_map_generation_from_arbitrary_files)
@@ -26,3 +32,4 @@ phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
 
  
 [[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
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