diff --git a/installation-linux/README.md b/installation-linux/README.md
index 9b2aba4..1074c26 100644
--- a/installation-linux/README.md
+++ b/installation-linux/README.md
@@ -35,6 +35,7 @@ micromamba install python=3.11 -y
 micromamba install pymol-open-source -y
 micromamba install rdkit numpy scipy -y
 micromamba install chemicalite matplotlib=3.7 pandas -y
+micromamba install gemmi -y
 ```
 
 Several packages are being installed in a single line.
@@ -53,14 +54,14 @@ Running the following commands will install meeko and ringtail in
 the currently active micromamba environment.
 
 ```
-pip install meeko==0.6.0a3
 pip install ringtail
+pip install meeko==0.6.0a3
 ```
 
 Running the following commands should display help messages:
 ```
 mk_prepare_ligand.py
-rt_process_vs.py
+rt_process_vs -h
 ```
 
 A new release of Meeko will be available soon.
@@ -126,12 +127,12 @@ Copy the files in [toy-example-data](../toy-example-data) to the working dir and
 ```
 scrub.py "Oc1ccccc1" -o phenol.sdf
 mk_prepare_ligand.py -i phenol.sdf -o phenol.pdbqt
-mk_prepare_receptor.py --pdb pocket.pdb --ligand pocket.pdb --padding 5 -o receptor
+mk_prepare_receptor.py --read_pdb pocket.pdb --box_enveloping ligand.pdb --padding 5 -o receptor -p -j -v
 mkdir results
 ./vina_1.2.5_linux_x86_64 --receptor receptor.pdbqt --config receptor.box.txt --ligand phenol.pdbqt --out results/phenol.pdbqt
-rt_process_vs.py write -o results.db -fp results -m vina -ai -rf receptor.pdbqt
+rt_process_vs write -o results.db -fp results -m vina -ai -rf receptor.pdbqt -sr
 mkdir passing_sdf
-rt_process_vs.py read -i results.db -e -2 -sdf passing_sdf
+rt_process_vs read -i results.db -e -2 -sdf passing_sdf
 ```
 
 A file "phenol.sdf" should have been added to "passing\_sdf".