Merge pull request #90 from NDoering99/patch-24

Update README.md

README.md

@@ -109,9 +109,10 @@ Start the analysis with the following Inputs:
 
 -d = trajectory file of the simulation (in .dcd format)
 
-#### Optional:
 -n = Ligand name (3 letter code in PDB)
 
+#### Optional:
+
 -l = Ligand in SDF format
 
 -b = binding mode threshold. Is used to remove interactions under the defined procentual occurence from the binding mode generation. The default is 40% (accepted values: 0-100)
@@ -138,6 +139,8 @@ Start the analysis with the following Inputs:
 
 --watereps = the EPS of the clustering part during the water analysis. will only result in something if "-w True" is added. Accepts float (in Angstrom).
 
+--figure = File type for the figures, default is png. Can be changed to all file types supported by matplotlib.
+
 #### Command line example with default values
 
     openmmdl_analysis -t {path/to/topology} -d {path/to/trajectory} -n {Ligand_name}