From 734991fa70567d1a9b547cbbbb1985afc5ba78b3 Mon Sep 17 00:00:00 2001
From: Niklas Piet Doering <117102130+NDoering99@users.noreply.github.com>
Date: Wed, 24 Jul 2024 10:20:19 +0200
Subject: [PATCH] Update README.md

---
 README.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 954370e3..41bb9264 100644
--- a/README.md
+++ b/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}