model_map_generation.md

@@ -4,32 +4,10 @@ To produce the desired result of locally contrast-optimized maps, LocScale requi
 
 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.
   
 ```
-usage: prepare_locscale_input -mc model.pdb -em map.ccp4 [-dmin resolution] [-h]
-                 [--out OUT] [--table TABLE] [--apix APIX] [--radius RADIUS]
-                 [--bfactor BFACTOR] [--verbose]
-
-*** Computes reference map from PDB model and generates files for LocScale ***
-
-Input:
-  -mc model.pdb, --model model.pdb
-                              Input filename PDB
-  -em map.ccp4, --map map.ccp4
-                              Input filename map
-
-Options:
-  -dmin resolution            map resolution
-  -h, --help                  show this help message and exit
-  --out OUT                   Output filename RSCC table
-  --table TABLE               Scattering table [electron, itcc]
-  --apix APIX                 pixel size [A]
-  --radius RADIUS             atom radius [A]
-  --bfactor BFACTOR           set bfactor [A^2]
-  --verbose                   print result to stdout
-
+phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
 ```
   
 #### Link to [source](https://git.embl.de/jakobi/LocScale/blob/master/prepare_locscale_input.py)