diff --git a/.gitignore b/.gitignore
index 24c0589..b915a3b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ nanome_docking.egg-info/
 dist/
 *.pyc
 nanome
+nanome_docking/Rh_x64.exe
diff --git a/README.md b/README.md
index 2628f18..a958dc9 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # Nanome - Docking
 
-Plugin to dock ligands to a receptor and display the result in Nanome
+This Nanome plugin interfaces with a variety of docking softwares to dock ligands to a receptor and display the result in Nanome.
 
 ### Installation
 
@@ -33,6 +33,7 @@ In Nanome:
 - Click on "Ligand", and select ligands to dock
 - If using Smina, click on "Site", and select which molecule should be used to define the docking site
 - Choose exhaustiveness, number of results and size of the box to generate around the site molecule (Smina only)
+- If visual scoring is turned on, atom size and labels will indicate each atom's contribution to the ligand's score
 - Click on Run
 
 ### License
diff --git a/nanome_docking/Docking.py b/nanome_docking/Docking.py
index cbcbb85..c11f6a5 100644
--- a/nanome_docking/Docking.py
+++ b/nanome_docking/Docking.py
@@ -1,7 +1,10 @@
 import nanome
 from ._DockingCalculations import DockingCalculations as Smina
 from ._DockingCalculationsAutodock4 import DockingCalculations as Autodock4
+from ._DockingCalculationsRhodium import DockingCalculations as Rhodium
 from ._DockingMenu import DockingMenu
+from ._DockingMenuRhodium import DockingMenuRhodium
+import functools
 import sys
 
 __metaclass__ = type
@@ -19,32 +22,38 @@ def convert_atoms_to_relative_position(complex, mat):
 
 class Docking(nanome.PluginInstance):
     def __init__(self):
-        self._menu = DockingMenu(self)
+        self._menu = None
         self._calculations = None
         self._autobox = True
 
-    # Function called when Nanome connects to the Plugin, after its instantiation
+    # Called when Nanome connects to the Plugin, after its instantiation
     def start(self):
         self._menu.build_menu()
         if self._autobox == False:
             self._menu.disable_autobox()
+        # Request shallow complex (name, position, orientation), to display them in a list
         self.request_complex_list(self.on_complex_list_received)
 
-    # Function called when user clicks on the "Run" button in Nanome
+    # Called when user clicks on the "Run" button in Nanome
     def on_run(self):
         menu = self._menu
-        if menu._selected_receptor == None or menu._selected_site == None or menu._selected_ligands == []:
+        # If menu doesn't have Receptor and Ligands selected, open it
+        # Else, just start docking
+        if menu.is_ready_for_docking() == False:
             self.open_menu()
         else:
-            self.run_docking(menu._selected_receptor[1], menu._selected_ligands, menu._selected_site[1])
+            self.run_docking(menu.get_receptor(), menu.get_ligands(), menu.get_site(), menu.get_params())
 
+    # Called when user click on the "Advanced Settings" button in Nanome
     def on_advanced_settings(self):
         nanome.util.Logs.debug("Advanced Settings")
         self.open_menu()
 
+    # Called when a complex is added to the workspace in Nanome
     def on_complex_added(self):
         self.request_complex_list(self.on_complex_list_received)
 
+    # Called when a complex is removed from the workspace in Nanome
     def on_complex_removed(self):
         self.request_complex_list(self.on_complex_list_received)
 
@@ -56,38 +65,69 @@ def open_menu(self):
     def make_plugin_usable(self):
         self._menu.make_plugin_usable()
 
-    # Function called when Nanome returns the complex list after a request
     def on_complex_list_received(self, complexes):
         self._menu.change_complex_list(complexes)
 
-    def run_docking(self, receptor, ligand_list, site, params):
-        has_site = site != None
-
-        def on_complexes_received(complexes):
+    def combine_ligands_start_docking(self, receptor, site, params, individual_ligands):
+        combined_ligands = nanome.structure.Complex()
+        combined_ligands.names = []
+        for ligand in individual_ligands:
+                convert_atoms_to_absolute_position(ligand)
+                convert_atoms_to_relative_position(ligand, receptor.m_workspace_to_complex)
+                combined_ligands.names.append(ligand.name)
+                for molecule in ligand.molecules:
+                    combined_ligands.add_molecule(molecule)
+        self._calculations.start_docking(receptor, combined_ligands, site, **params)
+
+    def replace_conformer(self, complexes, callback, existing=True):
+        for i in range(len(complexes)):
+            complex_index = complexes[i].index
+            complexes[i] = complexes[i].convert_to_frames()
+            complexes[i].index = complex_index
+        
+        rerequest_complexes = functools.partial(self.request_complexes, [complex.index for complex in complexes], callback)
+
+        request_docking_results = functools.partial(self.request_docking_results, callback)
+        rerequest_complexes = functools.partial(self.request_complex_list, request_docking_results) if not existing else rerequest_complexes
+        
+        self.update_structures_deep(complexes, rerequest_complexes)
+
+    def request_docking_results(self, callback, all_complexes):
+        docking_results_index = all_complexes[len(all_complexes)-1].index
+        self.request_complexes([docking_results_index], callback)
+
+    def set_and_convert_structures(self, has_site, params, complexes):
+            # When deep complexes data are received, unpack them and prepare ligand for docking
             receptor = complexes[0]
+            receptor.m_workspace_to_complex = receptor.get_workspace_to_complex_matrix()
             self._receptor = receptor
-            m_workspace_to_receptor = receptor.get_workspace_to_complex_matrix()
             starting_lig_idx = 1
             site = None
             if has_site:
                 site = complexes[1]
                 self._site = site
                 convert_atoms_to_absolute_position(site)
-                convert_atoms_to_relative_position(site, m_workspace_to_receptor)
+                convert_atoms_to_relative_position(site, receptor.m_workspace_to_complex)
                 starting_lig_idx = 2
-            ligands = nanome.structure.Complex()
-            for ligand in complexes[starting_lig_idx:]:
-                convert_atoms_to_absolute_position(ligand)
-                convert_atoms_to_relative_position(ligand, m_workspace_to_receptor)
-                for molecule in ligand.molecules:
-                    ligands.add_molecule(molecule)
-            self._calculations.start_docking(receptor, ligands, site, **params)
-
+            # convert ligands to frame representation
+            ligands = complexes[starting_lig_idx:]
+            combine_ligs_and_start_docking = functools.partial(self.combine_ligands_start_docking, receptor, site, params)
+            self.replace_conformer(ligands, combine_ligs_and_start_docking)
+
+    def run_docking(self, receptor, ligands, site, params):
+        # Change the plugin to be "unusable"
+        if self._menu._run_button.unusable == True:
+            return
+        self._menu.make_plugin_usable(False)
+
+        # Request complexes to Nanome in this order: [receptor, site (if any), ligand, ligand,...]
         request_list = [receptor.index]
-        if has_site:
+        if site != None:
             request_list.append(site.index)
-        request_list += [x.index for x in ligand_list]
-        self.request_complexes(request_list, on_complexes_received)
+        request_list += [x.index for x in ligands]
+
+        setup_structures = functools.partial(self.set_and_convert_structures, site != None, params)
+        self.request_complexes(request_list, setup_structures)
 
     # Called every update tick of the Plugin
     def update(self):
@@ -121,14 +161,22 @@ class SminaDocking(Docking):
     def __init__(self):
         super(SminaDocking, self).__init__()
         self._calculations = Smina(self)
+        self._menu = DockingMenu(self)
 
 
 class Autodock4Docking(Docking):
     def __init__(self):
         super(Autodock4Docking, self).__init__()
         self._calculations = Autodock4(self)
+        self._menu = DockingMenu(self)
         self._autobox = False
 
+class RhodiumDocking(Docking):
+    def __init__(self):
+        super(RhodiumDocking, self).__init__()
+        self._calculations = Rhodium(self)
+        self._menu = DockingMenuRhodium(self)
+
 
 def main():
     name = None
@@ -140,8 +188,11 @@ def main():
         elif arg == "autodock4":
             name = "Autodock 4"
             cl = Autodock4Docking
+        elif arg == "rhodium":
+            name = "Rhodium"
+            cl = RhodiumDocking
     if name == None:
-        nanome.util.Logs.error("Please pass the docking software to use as an argument: smina|autodock4")
+        nanome.util.Logs.error("Please pass the docking software to use as an argument: smina|autodock4|rhodium")
         sys.exit(1)
 
     # Create the plugin, register Docking as the class to instantiate, and start listening
diff --git a/nanome_docking/_DockingCalculations.py b/nanome_docking/_DockingCalculations.py
index c96c32e..60a4f59 100644
--- a/nanome_docking/_DockingCalculations.py
+++ b/nanome_docking/_DockingCalculations.py
@@ -1,7 +1,9 @@
 import traceback
-
+import math
+import re
 import nanome
 import shutil
+import gzip
 import itertools
 import operator
 import os
@@ -12,6 +14,8 @@
 
 from nanome.util.enums import NotificationTypes
 
+DEBUG = True
+
 SDFOPTIONS = nanome.api.structure.Complex.io.SDFSaveOptions()
 SDFOPTIONS.write_bonds = True
 PDBOPTIONS = nanome.api.structure.Complex.io.PDBSaveOptions()
@@ -23,18 +27,6 @@
 except:
     pass
 
-def not_dollars(line):
-    return '$$$$' != line.strip('\n')
-
-def parse_molecules(file, self):
-    nanome.util.Logs.debug("Parsing output", file)
-    with open(file) as lines:
-        while True:
-            block = list(itertools.takewhile(not_dollars, lines ))
-            if not block:
-                break
-            yield block + ['$$$$\n']
-
 class DockingCalculations():
     def __init__(self, plugin):
         self._plugin = plugin
@@ -42,20 +34,19 @@ def __init__(self, plugin):
         self._running = False
         self._structures_written = False
         self._started_docking = False
+        self.requires_site = True
 
 
     def initialize(self):
         self.temp_dir = tempfile.TemporaryDirectory()
         self._receptor_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
         self._ligands_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
-        self._ligands_pdb_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
         self._site_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
         self._docking_output = tempfile.NamedTemporaryFile(delete=False, prefix="output", suffix=".sdf", dir=self.temp_dir.name)
         self._ligand_output = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
         self._log_file = tempfile.NamedTemporaryFile(delete=False, dir=self.temp_dir.name)
 
-
-    def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, replace, scoring, autobox):
+    def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, replace, scoring, visual_scores, autobox):
         self._exhaustiveness = exhaustiveness
         self._modes = modes
         self._receptor = receptor
@@ -64,6 +55,7 @@ def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, r
         self._align = align
         self._replace = replace
         self._scoring = scoring
+        self._visual_scores = visual_scores
         self._autobox = autobox
 
         # Start docking process
@@ -92,9 +84,9 @@ def write_structures_to_file(self):
         self._receptor.io.to_pdb(self._receptor_input.name, PDBOPTIONS)
         nanome.util.Logs.debug("Saved PDB", self._receptor_input.name)
         self._ligands.io.to_pdb(self._ligands_input.name, PDBOPTIONS)
-        nanome.util.Logs.debug("Saved SDF", self._ligands_input.name)
+        nanome.util.Logs.debug("Saved PDB", self._ligands_input.name)
         self._site.io.to_pdb(self._site_input.name, PDBOPTIONS)
-        nanome.util.Logs.debug("Saved SDF", self._site_input.name)
+        nanome.util.Logs.debug("Saved PDB", self._site_input.name)
         
     def _check_conversion(self):
         poll = self._obabel_process.poll()
@@ -104,12 +96,14 @@ def _check_conversion(self):
 
     def _start_docking(self):
         exe_path = os.path.join(os.path.dirname(__file__), 'smina')
-
+        
         if self._scoring:
             smina_args = [exe_path, '-r', self._receptor_input.name, '-l', self._ligands_input.name, '--autobox_ligand', self._site_input.name, '--score_only', '--out', self._ligand_output.name]
         else:
+
             smina_args = [exe_path, '-r', self._receptor_input.name, '-l', self._ligands_input.name, '--autobox_ligand', self._site_input.name, '--out', \
-                self._docking_output.name, '--log', self._log_file.name, '--exhaustiveness', str(self._exhaustiveness), '--num_modes', str(self._modes), '--autobox_add', str(self._autobox), '--seed', '0']
+                self._docking_output.name, '--log', self._log_file.name, '--exhaustiveness', str(self._exhaustiveness), '--num_modes', str(self._modes), '--autobox_add', str(self._autobox), '--atom_term_data']
+        
         nanome.util.Logs.debug("Run SMINA")
         self._start_timer = timer()
         try:
@@ -128,54 +122,85 @@ def _start_docking(self):
     def _check_docking(self):
         return self._smina_process.poll() != None
 
-    def _reassemble_ligs(self):
-        generators = parse_molecules(self._docking_output.name, self)
-        fout = open(self._ligand_output.name, 'w')
-            
-        try:
-            for gen in generators:
-                for line in gen:
-                    str = lines.strip('\n')
-                    fout.write(''.join(str))
-                    fout.write('\n')
-        except StopIteration:
-            pass
-                
-        fout.close()
-    
-    def _docking_finished(self):
-        end = timer()
-        nanome.util.Logs.debug("Docking Finished in", end - self._start_timer, "seconds")
-        self._request_pending = False
-        try:
-            (results, errors) = self._smina_process.communicate()
-            if len(errors) == 0:
-                for line in results.decode().splitlines():
-                    nanome.util.Logs.debug(line)
-            else:
-                for line in errors.decode().splitlines():
-                    nanome.util.Logs.warning(line)
-        except:
-            nanome.util.Logs.warning(traceback.format_exc())
+    def _resume_docking_finished(self, docking_results):
+        docking_results = docking_results[0]
+        nanome.util.Logs.debug("Read SDF", self._docking_output.name)
+        for i, molecule in enumerate(docking_results.molecules):
+            nanome.util.Logs.debug("molecule " + str(i))
+            self.set_scores(i, molecule)
 
-        if not self._scoring:
-            pass
-            # self._reassemble_ligs()
-        docked_ligands = nanome.structure.Complex.io.from_sdf(path=self._docking_output.name)
-        nanome.util.Logs.debug("Read PDB", self._docking_output.name)
+        if self._visual_scores:
+            self.visualize_scores(docking_results)
 
         if not self._scoring:
-            docked_ligands.molecular.name = "Docking"
-            docked_ligands.rendering.visible = True
+            if len(self._ligands.names) > 1:
+                docking_results.name += "Docking Results"
+            elif len(self._ligands.names) == 1:
+                docking_results.name = self._ligands.names[0] + " (Docked)"
+            docking_results.visible = True
             
-        self._plugin.make_plugin_usable()
         if self._scoring:
             nanome.util.Logs.debug("Display scoring result")
-            self._plugin.display_scoring_result(docked_ligands)
+            self._plugin.display_scoring_result(docking_results)
         else:
             nanome.util.Logs.debug("Update workspace")
-            self._plugin.add_result_to_workspace([docked_ligands], self._align)
+            self._plugin.add_result_to_workspace([docking_results], self._align)
 
         shutil.rmtree(self.temp_dir.name)
 
         self._plugin.send_notification(NotificationTypes.success, "Docking finished")
+    
+    def _docking_finished(self):
+        end = timer()
+        nanome.util.Logs.debug("Docking Finished in", end - self._start_timer, "seconds")
+        self._request_pending = False
+
+        docking_results = nanome.structure.Complex.io.from_sdf(path=self._docking_output.name)
+        docking_results.index = 0
+        self._plugin.replace_conformer([docking_results], self._resume_docking_finished, existing=False)
+
+    def update_min_max_scores(self, molecule, score):
+        min_score = molecule.min_atom_score
+        max_score = molecule.max_atom_score
+        molecule.min_atom_score = score if score < min_score else min_score
+        molecule.max_atom_score = score if score > max_score else max_score
+
+    def set_scores(self, lig_i, molecule):
+        molecule.min_atom_score = float('inf')
+        molecule.max_atom_score = float('-inf')
+
+        num_rgx = '(-?[\d.]+(?:e[+-]\d+)?)'
+        pattern = re.compile('<{},{},{}> {} {} {} {} {}'.format(*([num_rgx] * 8)), re.U)
+        for associated in molecule.associateds:
+            pose_score = associated['> <minimizedAffinity>']
+            for residue in molecule.residues:
+                residue.label_text = pose_score + " kcal/mol"
+                residue.labeled = True
+            interaction_terms = associated['> <atomic_interaction_terms>']
+            interaction_values = re.findall(pattern, interaction_terms)
+            atom_count = len([atom for atom in molecule.atoms])
+            for i, atom in enumerate(molecule.atoms):
+                if i < len(interaction_values) - 1:
+                    nanome.util.Logs.debug("interaction values for atom " + str(i) + ": "+ str(interaction_values[i]))
+                    atom.score = float(interaction_values[i][5])
+                    self.update_min_max_scores(molecule, atom.score)
+
+    
+    def visualize_scores(self, ligand_complex):
+        for molecule in ligand_complex.molecules:
+            for atom in molecule.atoms:
+                if hasattr(atom, "score"):
+                    atom.atom_mode = nanome.api.structure.Atom.AtomRenderingMode.Point
+                    denominator = -molecule.min_atom_score if atom.score < 0 else molecule.max_atom_score
+                    norm_score = atom.score / denominator
+                    atom.atom_scale = norm_score * 1.5 + 0.1
+                    atom.label_text = self.truncate(atom.score, 3)
+                    atom.labeled = True
+
+    def truncate(self, f, n):
+        '''Truncates/pads a float f to n decimal places without rounding'''
+        s = '{}'.format(f)
+        if 'e' in s or 'E' in s:
+            return '{0:.{1}f}'.format(f, n)
+        i, p, d = s.partition('.')
+        return '.'.join([i, (d+'0'*n)[:n]])
\ No newline at end of file
diff --git a/nanome_docking/_DockingCalculationsAutodock4.py b/nanome_docking/_DockingCalculationsAutodock4.py
index 0f8f797..d8b4584 100644
--- a/nanome_docking/_DockingCalculationsAutodock4.py
+++ b/nanome_docking/_DockingCalculationsAutodock4.py
@@ -1,5 +1,6 @@
 import nanome
 import os
+import shutil
 import subprocess
 import tempfile
 import re
@@ -21,21 +22,23 @@ def __init__(self, plugin):
         self._pdb_options.write_bonds = True
         self._sdf_options = SDFOptions()
         self._sdf_options.write_bonds = True
+        self.requires_site = False
 
     def initialize(self):
         # TODO: Read and write in a folder unique per plugin instance
-        self._protein_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
-        self._protein_input_converted = tempfile.NamedTemporaryFile(delete=False, suffix=".pdbqt")
-        self._ligands_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
-        self._ligands_input_converted = tempfile.NamedTemporaryFile(delete=False, suffix=".pdbqt")
-        self._ligands_output = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
-        self._bond_output = tempfile.NamedTemporaryFile(delete=False, suffix=".sdf")
-        self._autogrid_input = tempfile.NamedTemporaryFile(delete=False, suffix=".gpf")
-        self._autodock_input = tempfile.NamedTemporaryFile(delete=False, suffix=".dpf")
-        self._autogrid_log = tempfile.NamedTemporaryFile(delete=False, suffix=".glg")
-        self._autodock_log = tempfile.NamedTemporaryFile(delete=False, suffix=".dlf")
-
-    def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, replace, scoring, autobox):
+        self.temp_dir = tempfile.TemporaryDirectory()
+        self._protein_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
+        self._protein_input_converted = tempfile.NamedTemporaryFile(delete=False, suffix=".pdbqt", dir=self.temp_dir.name)
+        self._ligands_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
+        self._ligands_input_converted = tempfile.NamedTemporaryFile(delete=False, suffix=".pdbqt", dir=self.temp_dir.name)
+        self._ligands_output = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb", dir=self.temp_dir.name)
+        self._bond_output = tempfile.NamedTemporaryFile(delete=False, suffix=".sdf", dir=self.temp_dir.name)
+        self._autogrid_input = tempfile.NamedTemporaryFile(delete=False, suffix=".gpf", dir=self.temp_dir.name)
+        self._autodock_input = tempfile.NamedTemporaryFile(delete=False, suffix=".dpf", dir=self.temp_dir.name)
+        self._autogrid_log = tempfile.NamedTemporaryFile(delete=False, suffix=".glg", dir=self.temp_dir.name)
+        self._autodock_log = tempfile.NamedTemporaryFile(delete=False, suffix=".dlf", dir=self.temp_dir.name)
+
+    def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, replace, scoring, visual_scores, autobox):
         self.initialize()
         # Save all input files
         receptor.io.to_pdb(self._protein_input.name, self._pdb_options)
@@ -44,9 +47,11 @@ def start_docking(self, receptor, ligands, site, exhaustiveness, modes, align, r
         nanome.util.Logs.debug("Saved PDB", self._ligands_input.name)
 
         self._receptor = receptor
+        self._ligands = ligands
         self._site = site
         self._align = align
         self._replace = replace
+        self._visual_scores = visual_scores
 
         # Start docking process
         self._running = False
@@ -123,13 +128,13 @@ def _check_process_error(self, process, check_only_errors = False):
 
     def _start_preparation(self):
         # Awful situation here
-        lig_args = ['py', '-2.5', os.path.join(os.path.dirname(__file__), 'prepare_ligand4.py'), '-l', self._ligands_input.name, '-o', self._ligands_input_converted.name]
-        rec_args = ['py', '-2.5', os.path.join(os.path.dirname(__file__), 'prepare_receptor4.py'), '-r', self._protein_input.name, '-o', self._protein_input_converted.name]
+        lig_args = ['python', os.path.join(os.path.dirname(__file__), 'prepare_ligand4.py'), '-l', self._ligands_input.name, '-o', self._ligands_input_converted.name]
+        rec_args = ['python', os.path.join(os.path.dirname(__file__), 'prepare_receptor4.py'), '-r', self._protein_input.name, '-o', self._protein_input_converted.name]
 
         nanome.util.Logs.debug("Prepare ligand and receptor")
         self._start_timer = timer()
-        self._lig_process = subprocess.Popen(lig_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._rec_process = subprocess.Popen(rec_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        self._lig_process = subprocess.Popen(lig_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=self.temp_dir.name)
+        self._rec_process = subprocess.Popen(rec_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=self.temp_dir.name)
         self._running = True
 
     def _check_preparation(self):
@@ -150,13 +155,13 @@ def _preparation_finished(self):
 
     def _start_parameters_preparation(self):
         # Awful situation here
-        grid_args = ['py', '-2.5', os.path.join(os.path.dirname(__file__), 'prepare_gpf4.py'), '-l', self._ligands_input_converted.name, '-r', self._protein_input_converted.name, '-o', self._autogrid_input.name]
-        dock_args = ['py', '-2.5', os.path.join(os.path.dirname(__file__), 'prepare_dpf42.py'), '-l', self._ligands_input_converted.name, '-r', self._protein_input_converted.name, '-o', self._autodock_input.name]
+        grid_args = ['python', os.path.join(os.path.dirname(__file__), 'prepare_gpf4.py'), '-l', self._ligands_input_converted.name, '-r', self._protein_input_converted.name, '-o', self._autogrid_input.name]
+        dock_args = ['python', os.path.join(os.path.dirname(__file__), 'prepare_dpf42.py'), '-l', self._ligands_input_converted.name, '-r', self._protein_input_converted.name, '-o', self._autodock_input.name]
 
         nanome.util.Logs.debug("Prepare grid and docking parameter files")
         self._start_timer = timer()
-        self._grid_process = subprocess.Popen(grid_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        self._dock_process = subprocess.Popen(dock_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        self._grid_process = subprocess.Popen(grid_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=self.temp_dir.name)
+        self._dock_process = subprocess.Popen(dock_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=self.temp_dir.name)
         self._running = True
 
     def _check_parameters_preparation(self):
@@ -181,15 +186,10 @@ def _parameters_preparation_finished(self):
 
     def _start_grid(self):
         full_name = self._autogrid_input.name
-        delimiter = full_name.rfind('\\')
-        path = full_name[:delimiter]
-        name = full_name[delimiter + 1:]
-
         full_name_log = self._autogrid_log.name
-        delimiter_log = full_name_log.rfind('\\')
-        name_log = full_name_log[delimiter_log + 1:]
+        path = os.path.dirname(full_name)
 
-        args = ['autogrid4', '-p', name, '-l', name_log]
+        args = ['autogrid4', '-p', full_name, '-l', full_name_log]
 
         nanome.util.Logs.debug("Start Autogrid")
         self._start_timer = timer()
@@ -214,15 +214,10 @@ def _grid_finished(self):
 
     def _start_docking(self):
         full_name_input = self._autodock_input.name
-        delimiter_input = full_name_input.rfind('\\')
-        path = full_name_input[:delimiter_input]
-        name_input = full_name_input[delimiter_input + 1:]
-
+        path = os.path.dirname(full_name_input)
         full_name_log = self._autodock_log.name
-        delimiter_log = full_name_log.rfind('\\')
-        name_log = full_name_log[delimiter_log + 1:]
 
-        args = ['autodock4', '-p', name_input, '-l', name_log]
+        args = ['autodock4', '-p', full_name_input, '-l', full_name_log]
 
         nanome.util.Logs.debug("Start Autodock")
         self._start_timer = timer()
@@ -291,12 +286,15 @@ def _bonds_finished(self):
         docked_ligands = nanome.structure.Complex.io.from_sdf(path=self._bond_output.name)
         nanome.util.Logs.debug("Read SDF", self._bond_output.name)
 
-        docked_ligands.molecular.name = "Docking"
-        docked_ligands.rendering.visible = True
+        docked_ligands.name = self._ligands[0].full_name + " (Docked)"
+        docked_ligands.visible = True
         if self._align == True:
             docked_ligands.transform.position = self._receptor.transform.position
             docked_ligands.transform.rotation = self._receptor.transform.rotation
 
         nanome.util.Logs.debug("Update workspace")
-        self._plugin.make_plugin_usable()
-        self._plugin.add_result_to_workspace([docked_ligands])
\ No newline at end of file
+        # TODO: verify this shouldn't be here anymore (test)
+        # self._plugin.make_plugin_usable()
+        self._plugin.add_result_to_workspace([docked_ligands])
+
+        shutil.rmtree(self.temp_dir.name)
\ No newline at end of file
diff --git a/nanome_docking/_DockingCalculationsRhodium.py b/nanome_docking/_DockingCalculationsRhodium.py
new file mode 100644
index 0000000..b015dd0
--- /dev/null
+++ b/nanome_docking/_DockingCalculationsRhodium.py
@@ -0,0 +1,179 @@
+import nanome
+from nanome.util import Logs, Process
+from nanome.util.enums import NotificationTypes
+
+import os
+import tempfile
+import traceback
+import subprocess
+from timeit import default_timer as timer
+
+RHODIUM_PATH = os.path.join(os.path.dirname(__file__), 'Rh_x64.exe')
+
+class DockingCalculations():
+    def __init__(self, plugin):
+        self._plugin = plugin
+        self.__docking_running = False
+        self.requires_site = False
+
+    # Entry point, where everything starts
+    def start_docking(self, receptor, ligands, site, params):
+        # Create temporary files
+        self.initialize()
+
+        self._ligands = ligands
+        self._receptor = receptor
+        self._site = site
+        self._params = params
+
+        self.prepare_receptor(receptor)
+
+    # Docking process needs to be check manually in an update loop for now
+    # This is due to a current bug with the plugin system Process API with process outputting a lot of text
+    # In the future, no update loop will be needed to check when Rhodium has ended
+    def update(self):
+        if self.__docking_running == False:
+            return
+
+        self.__process.communicate()
+        if self.__process.poll() != None:
+            self.__docking_running = False
+            self._docking_finished()
+
+    def initialize(self):
+        self._protein_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
+        self._protein_converted_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
+        self._ligands_input = tempfile.NamedTemporaryFile(delete=False, suffix=".sdf")
+        self._site_input = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
+        self._docking_output = tempfile.NamedTemporaryFile()
+        self._docking_output.close()
+
+    def clean_files(self, docking_result):
+        self._protein_input.close()
+        self._protein_converted_input.close()
+        self._ligands_input.close()
+        self._site_input.close()
+        os.remove(self._protein_input.name)
+        os.remove(self._protein_converted_input.name)
+        os.remove(self._ligands_input.name)
+        os.remove(self._site_input.name)
+        os.remove(self._docking_output.name + ".csv")
+        for entry in docking_result:
+            os.chmod(entry[0], 0o777)
+            os.remove(entry[0])
+        pass
+
+    def prepare_receptor(self, receptor):
+        # Remove waters
+        residues_to_remove = []
+        for residue in receptor.residues:
+            if residue.name == "HOH":
+                residues_to_remove.append(residue)
+
+        for residue in residues_to_remove:
+            residue.parent.remove_residue(residue)
+
+        # Write pdb file for openbabel
+        receptor.io.to_pdb(self._protein_input.name)
+
+        # Use openbabel to add hydrogens
+        proc = Process()
+        proc.executable_path = 'obabel'
+        proc.args = ['-ipdb', self._protein_input.name,
+            '-opdb', '-O' + self._protein_converted_input.name, '-h']
+        proc.on_done = self.receptor_ready
+        proc.start()
+
+    # Callback when obabel is done
+    def receptor_ready(self, return_value):
+        self._ligands.io.to_sdf(self._ligands_input.name)
+        if self._site != None:
+            self._site.io.to_sdf(self._site_input.name)
+        self._start_docking()
+
+    def _start_docking(self):
+        # Start process manually, because of problem described above Update function
+        args = [RHODIUM_PATH, self._protein_converted_input.name, self._ligands_input.name,
+            '--outfile', self._docking_output.name,
+            '--refine', str(self._params['poses']),
+            '--resolution', str(self._params['grid_resolution']),
+            '--refine', str(self._params['poses']),
+            '--nr', str(self._params['rotamers'])]
+
+        if self._params['ignore_hetatoms']:
+            args += ['--ignore_pdb_hetatm']
+
+        if self._site != None:
+            args += ['--usegrid', self._site_input.name]
+
+        Logs.debug("Start Rhodium:", args)
+
+        self._start_timer = timer()
+        try:
+            self.__process = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=os.path.dirname(__file__))
+        except:
+            nanome.util.Logs.error("Couldn't execute Rhodium, please check if executable is in the plugin folder and has permissions. Path:", RHODIUM_PATH, traceback.format_exc())
+            self._plugin.make_plugin_usable()
+            self._plugin.send_notification(NotificationTypes.error, "Docking error, check plugin")
+            return
+
+        self._plugin.send_notification(NotificationTypes.message, "Docking started")
+        self.__docking_running = True
+
+    def read_csv(self):
+        result = []
+        with open(self._docking_output.name + ".csv", 'r') as file:
+            lines = file.readlines()
+            for line in lines:
+                if line.startswith('seed') == False:
+                    continue
+                line_split = line.split(',')
+                result.append([line_split[5].strip(),
+                    line_split[13].strip(),
+                    line_split[41].strip(),
+                    line_split[43].strip()])
+        return result
+
+    def assemble_result(self, docking_output):
+        # docking_output contains the lines from the csv file
+
+        docked_ligands = nanome.api.structure.Complex()
+        for entry in docking_output:
+            # Read complex from pdb and extract molecule from it
+            complex = nanome.structure.Complex.io.from_pdb(path=entry[0])
+            molecule = next(complex.molecules)
+            # Write docking information in the molecule
+            molecule._associated['score'] = entry[1]
+            molecule._associated['affinity'] = entry[2]
+            molecule._associated['pose_population'] = entry[3]
+            # Add it to the result complex
+            docked_ligands.add_molecule(molecule)
+
+        def bonds_added(complex_arr):
+            docked_ligands_bonded = complex_arr[0]
+            docked_ligands_bonded.name = "Docking"
+            docked_ligands_bonded.visible = True
+            if self._params['align'] == True:
+                docked_ligands_bonded.transform.position = self._receptor.transform.position
+                docked_ligands_bonded.transform.rotation = self._receptor.transform.rotation
+                docked_ligands_bonded.boxed = True
+
+            nanome.util.Logs.debug("Update workspace")
+            self._plugin.add_result_to_workspace([docked_ligands_bonded])
+
+            # Docking process is over, clean files and make plugin available again
+            self.clean_files(docking_output)
+            # TODO: Verify this shouldn't be here anymore (test)
+            # self._plugin.make_plugin_usable(True)
+            self._plugin.send_notification(NotificationTypes.success, "Docking finished")
+
+        # Add bonds to the result complex
+        self._plugin.add_bonds([docked_ligands], bonds_added)
+
+    def _docking_finished(self):
+        end = timer()
+        nanome.util.Logs.debug("Docking Finished in", end - self._start_timer, "seconds")
+
+        # When Rhodium finished, read csv, then assemble result ligands
+        docking_output = self.read_csv()
+        self.assemble_result(docking_output)
diff --git a/nanome_docking/_DockingMenu.py b/nanome_docking/_DockingMenu.py
index 099e5c3..7699c74 100644
--- a/nanome_docking/_DockingMenu.py
+++ b/nanome_docking/_DockingMenu.py
@@ -9,14 +9,15 @@ def __init__(self, docking_plugin):
         self._selected_receptor = None
         self._selected_ligands = []
         self._selected_site = None
-        self._exhaustiveness = 8
-        self._modes = 9
+        self._exhaustiveness = 10
+        self._modes = 5
         self._autobox = 4
         self._run_button = None
         self._run_button = None
         self._align = True
         self._replace = False
         self._scoring = False
+        self._visual_scores = False
         self._tab = None
         self._autobox_enabled = True
     
@@ -27,6 +28,27 @@ def get_params(self):
             params[key] = newvalue
         return params
 
+    def get_receptor(self):
+        return self._selected_receptor.complex
+
+    def get_ligands(self):
+        ligands = []
+        for item in self._selected_ligands:
+            ligands.append(item.complex)
+        return ligands
+
+    def get_site(self):
+        if self._selected_site == None:
+            return None
+        return self._selected_site.complex
+
+    def get_params(self):
+        params = {"exhaustiveness": None, "modes": None, "align": None, "replace": None, "scoring": None, "visual_scores": None, "autobox": None}
+        for key, value in params.items():
+            newvalue = getattr(self, "_"+key)
+            params[key] = newvalue
+        return params
+
     def _run_docking(self):
         if self._selected_receptor == None or len(self._selected_ligands) == 0:
             if self._autobox_enabled == True and self._selected_site == None:
@@ -50,7 +72,7 @@ def disable_autobox(self):
         self._plugin.update_menu(self._menu)
 
     def make_plugin_usable(self, state=True):
-        self._run_button.unusable = not state | self.refresh_run_btn_enabled(False)
+        self._run_button.unusable = (not state) | self.refresh_run_btn_unusable(False)
         self._plugin.update_content(self._run_button)
 
     def receptor_pressed(self, button):
@@ -64,7 +86,7 @@ def receptor_pressed(self, button):
         self._receptor_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'checkmark.png')
         self._plugin.update_content(self._receptor_checkmark)
 
-        self.refresh_run_btn_enabled()
+        self.refresh_run_btn_unusable()
 
     def ligand_pressed(self, button):
         if button.selected == False:
@@ -80,7 +102,7 @@ def ligand_pressed(self, button):
             self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
         self._plugin.update_content(self._ligand_checkmark)
 
-        self.refresh_run_btn_enabled()
+        self.refresh_run_btn_unusable()
 
     def site_pressed(self, button):
         lastSelected = self._selected_site
@@ -93,10 +115,11 @@ def site_pressed(self, button):
         self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'checkmark.png')
         self._plugin.update_content(self._site_checkmark)
         
-        self.refresh_run_btn_enabled()
+        self.refresh_run_btn_unusable()
     
-    def refresh_run_btn_enabled(self, update=True):
-        if self._selected_receptor != None and len(self._selected_ligands) > 0 and self._selected_site != None:
+    def refresh_run_btn_unusable(self, update=True):
+        site_requirement_met = self._selected_site != None or not self._plugin._calculations.requires_site
+        if self._selected_receptor != None and len(self._selected_ligands) > 0 and site_requirement_met:
             self._run_button.text.value_unusable = "Running..."
             self._run_button.unusable = False
         else:
@@ -117,13 +140,7 @@ def complex_pressed(button):
             elif self._tab.text.value_idle == "Site":
                 self.site_pressed(button)
 
-        self._selected_receptor = None
-        self._selected_ligands = []
-        self._selected_site = None
-        self._complex_list.items = []
-        self._receptor_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
-        self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
-        self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self.reset(update_menu=False)
 
         for complex in complex_list:
             clone = self._complex_item_prefab.clone()
@@ -137,23 +154,32 @@ def complex_pressed(button):
         self._plugin.update_menu(self._menu)
 
     def display_scoring_result(self, result):
-        self.reset_menu()
+        self.reset()
 
         for molecule in result.molecules:
             clone = self._score_item_prefab.clone()
             ln_lbl = clone.get_children()[0]
             lbl = ln_lbl.get_content()
-            lbl.text_value = molecule.molecular.name + " - " + molecule._associated["> <minimizedAffinity>"]
+            lbl.text_value = molecule.name + " - " + molecule._associated["> <minimizedAffinity>"]
             self._score_list.items.append(clone)
 
-    def reset_menu(self):
+    def reset(self, update_menu=True):
         self._selected_receptor = None
         self._selected_ligands = []
-        self._selected_site == None
+        self._selected_site = None
+        self._complex_list.items = []
+        self._receptor_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
 
         self.make_plugin_usable()
         self._plugin.update_menu(self._menu)
 
+    def open_menu(self):
+        self._plugin.menu = self._menu
+        self._plugin.menu.enabled = True
+        self._plugin.update_menu(self._plugin.menu)
+
     def build_menu(self):
         # defining callbacks
         def run_button_pressed_callback(button):
@@ -238,6 +264,11 @@ def scoring_button_pressed_callback(button):
             button.selected = self._scoring
             self._plugin.update_content(button)
 
+        def visual_scores_button_pressed_callback(button):
+            self._visual_scores = not self._visual_scores
+            button.selected = self._visual_scores
+            self._plugin.update_content(button)
+
         # Create a prefab that will be used to populate the lists
         self._complex_item_prefab = nanome.ui.LayoutNode()
         self._complex_item_prefab.layout_orientation = nanome.ui.LayoutNode.LayoutTypes.horizontal
@@ -298,6 +329,9 @@ def scoring_button_pressed_callback(button):
         self._score_btn = menu.root.find_node("ScoringButton", True).get_content()
         self._score_btn.register_pressed_callback(scoring_button_pressed_callback)
 
+        self._display_score_btn = menu.root.find_node("VisualScoresButton", True).get_content()
+        self._display_score_btn.register_pressed_callback(visual_scores_button_pressed_callback)
+
         close_score_btn = menu.root.find_node("CloseScoreButton", True).get_content()
         close_score_btn.register_pressed_callback(close_score_pressed_callback)
 
@@ -305,7 +339,7 @@ def scoring_button_pressed_callback(button):
         run_button.register_pressed_callback(run_button_pressed_callback)
         self._run_button = run_button
         self._run_button.enabled = False
-        self.refresh_run_btn_enabled()
+        self.refresh_run_btn_unusable()
 
         # lists
         self._complex_list = menu.root.find_node("ComplexList", True).get_content()
diff --git a/nanome_docking/_DockingMenuRhodium.py b/nanome_docking/_DockingMenuRhodium.py
new file mode 100644
index 0000000..097c728
--- /dev/null
+++ b/nanome_docking/_DockingMenuRhodium.py
@@ -0,0 +1,267 @@
+import nanome
+from nanome.api.ui.image import Image as Image
+
+import os
+
+class DockingMenuRhodium():
+    def __init__(self, docking_plugin):
+        self._plugin = docking_plugin
+        self._selected_receptor = None
+        self._selected_ligands = []
+        self._selected_site = None
+        self._grid_resolution = 2.5
+        self._poses = 128
+        self._rotamer = 6
+        self._run_button = None
+        self._align = True
+        self._ignore_hetatoms = False
+        self._tab = None
+
+    def is_ready_for_docking(self):
+        return self._selected_receptor != None and len(self._selected_ligands) > 0
+
+    def get_receptor(self):
+        return self._selected_receptor.complex
+
+    def get_ligands(self):
+        ligands = []
+        for item in self._selected_ligands:
+            ligands.append(item.complex)
+        return ligands
+
+    def get_site(self):
+        if self._selected_site == None:
+            return None
+        return self._selected_site.complex
+
+    def get_params(self):
+        return { "receptor":self._selected_receptor,
+                "ligands":self._selected_ligands,
+                "site":self._selected_site,
+                "grid_resolution":self._grid_resolution,
+                "poses":self._poses,
+                "rotamers":self._rotamer,
+                "align":self._align,
+                "ignore_hetatoms":self._ignore_hetatoms
+            }
+
+    def _run_docking(self):
+        if self._selected_receptor == None or len(self._selected_ligands) == 0:
+            nanome.util.Logs.warning("Trying to run docking without having one receptor, and at least one ligand selected")
+            self._plugin.send_notification(nanome.util.enums.NotificationTypes.error, "Please select a receptor, and at least one ligand")
+            return
+        ligands = []
+        for item in self._selected_ligands:
+            ligands.append(item.complex)
+        self._plugin.run_docking(self.get_receptor(), self.get_ligands(), self.get_site(), self.get_params())
+
+    def make_plugin_usable(self, state=True):
+        self._run_button.unusable = not state
+        self._plugin.update_content(self._run_button)
+
+    def receptor_pressed(self, button):
+        lastSelected = self._selected_receptor
+        if lastSelected != None:
+            lastSelected.selected = False
+            self._plugin.update_content(lastSelected)
+        button.selected = True
+        self._selected_receptor = button
+        self._plugin.update_content(button)
+        self._receptor_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'checkmark.png')
+        self._plugin.update_content(self._receptor_checkmark)
+
+    def ligand_pressed(self, button):
+        if button.selected == False:
+            button.selected = True
+            self._selected_ligands.append(button)
+        else:
+            button.selected = False
+            self._selected_ligands.remove(button)
+        self._plugin.update_content(button)
+        if len(self._selected_ligands) != 0:
+            self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'checkmark.png')
+        else:
+            self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self._plugin.update_content(self._ligand_checkmark)
+
+    def site_pressed(self, button):
+        lastSelected = self._selected_site
+        if lastSelected == button:
+            button.selected = False
+            self._plugin.update_content(button)
+            self._selected_site = None
+            self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+            self._plugin.update_content(self._site_checkmark)
+            return
+        elif lastSelected != None:
+            lastSelected.selected = False
+            self._plugin.update_content(lastSelected)
+        button.selected = True
+        self._selected_site = button
+        self._plugin.update_content(button)
+        self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'checkmark.png')
+        self._plugin.update_content(self._site_checkmark)
+
+    def change_complex_list(self, complex_list):
+        def complex_pressed(button):
+            if self._tab.text.value_idle == "Receptor":
+                self.receptor_pressed(button)
+            elif self._tab.text.value_idle == "Ligand":
+                self.ligand_pressed(button)
+            elif self._tab.text.value_idle == "Site":
+                self.site_pressed(button)
+
+        self._selected_receptor = None
+        self._selected_ligands = []
+        self._selected_site = None
+        self._complex_list.items = []
+        self._receptor_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self._ligand_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        self._site_checkmark.file_path = os.path.join(os.path.dirname(__file__), 'none.png')
+
+        for complex in complex_list:
+            clone = self._complex_item_prefab.clone()
+            ln_btn = clone.get_children()[0]
+            btn = ln_btn.get_content()
+            btn.set_all_text(complex.name)
+            btn.complex = complex
+            btn.register_pressed_callback(complex_pressed)
+            self._complex_list.items.append(clone)
+
+        self._plugin.update_menu(self._menu)
+
+    def build_menu(self):
+        # defining callbacks
+        def run_button_pressed_callback(button):
+            self._run_docking()
+
+        def grid_resolution_changed(input):
+            try:
+                self._grid_resolution = float(input.input_text)
+                nanome.util.Logs.debug("Grid resolution set to", self._grid_resolution)
+            except:
+                self._grid_resolution = 1.4
+
+        def poses_changed(input):
+            try:
+                self._poses = int(input.input_text)
+                nanome.util.Logs.debug("Poses count set to", self._poses)
+            except:
+                self._poses = 96
+            if self._poses <= 0:
+                self._poses = 96
+
+        def rotamer_changed(input):
+            try:
+                self._rotamer = int(input.input_text)
+                nanome.util.Logs.debug("Rotamer count set to", self._rotamer)
+            except:
+                self._rotamer = 3
+            if self._rotamer <= 0:
+                self._rotamer = 3
+
+        def tab_button_pressed_callback(button):
+            if self._tab == button:
+                return
+
+            self._tab.selected = False
+            button.selected = True
+            self._tab = button
+
+            if button.text.value_idle == "Receptor":
+                for item in self._complex_list.items:
+                    btn = item.get_children()[0].get_content()
+                    if btn == self._selected_receptor:
+                        btn.selected = True
+                    else:
+                        btn.selected = False
+            elif button.text.value_idle == "Ligand":
+                for item in self._complex_list.items:
+                    btn = item.get_children()[0].get_content()
+                    if btn in self._selected_ligands:
+                        btn.selected = True
+                    else:
+                        btn.selected = False
+            elif button.text.value_idle == "Site":
+                for item in self._complex_list.items:
+                    btn = item.get_children()[0].get_content()
+                    if btn == self._selected_site:
+                        btn.selected = True
+                    else:
+                        btn.selected = False
+
+            self._plugin.update_menu(self._menu)
+
+        def align_button_pressed_callback(button):
+            self._align = not self._align
+            button.selected = self._align
+            self._plugin.update_content(button)
+
+        def ignore_hetatoms_pressed_callback(button):
+            self._ignore_hetatoms = not self._ignore_hetatoms
+            button.selected = self._ignore_hetatoms
+            self._plugin.update_content(button)
+
+        # Create a prefab that will be used to populate the lists
+        self._complex_item_prefab = nanome.ui.LayoutNode()
+        self._complex_item_prefab.layout_orientation = nanome.ui.LayoutNode.LayoutTypes.horizontal
+        child = self._complex_item_prefab.create_child_node()
+        child.forward_dist = 0.002
+        child.add_new_button()
+
+        # loading menus
+        menu = nanome.ui.Menu.io.from_json(os.path.join(os.path.dirname(__file__), '_docking_menu_rhodium.json'))
+        self._plugin.menu = menu
+
+        # images
+        none_path = os.path.join(os.path.dirname(__file__), 'none.png')
+        logo_path = os.path.join(os.path.dirname(__file__), 'swri_logo.png')
+        self._receptor_checkmark = menu.root.find_node("ReceptorIcon", True).add_new_image(none_path)
+        self._receptor_checkmark.scaling_option = Image.ScalingOptions.fit
+        self._ligand_checkmark = menu.root.find_node("LigandIcon", True).add_new_image(none_path)
+        self._ligand_checkmark.scaling_option = Image.ScalingOptions.fit
+        self._site_checkmark = menu.root.find_node("SiteIcon", True).add_new_image(none_path)
+        self._site_checkmark.scaling_option = Image.ScalingOptions.fit
+        logo_image = menu.root.find_node("LogoImage", True).add_new_image(logo_path)
+        logo_image.scaling_option = Image.ScalingOptions.fit
+
+        # texts
+        txt1 = menu.root.find_node("GridResolutionInput", True).get_content()
+        txt1.register_changed_callback(grid_resolution_changed)
+
+        txt2 = menu.root.find_node("PosesCountInput", True).get_content()
+        txt2.register_changed_callback(poses_changed)
+
+        txt3 = menu.root.find_node("RotamerCountInput", True).get_content()
+        txt3.register_changed_callback(rotamer_changed)
+
+        # buttons
+        receptor_btn = menu.root.find_node("ReceptorButton", True).get_content()
+        receptor_btn.register_pressed_callback(tab_button_pressed_callback)
+        receptor_btn.selected = True
+        self._tab = receptor_btn
+
+        ligand_btn = menu.root.find_node("LigandButton", True).get_content()
+        ligand_btn.register_pressed_callback(tab_button_pressed_callback)
+
+        site_btn = menu.root.find_node("SiteButton", True).get_content()
+        site_btn.register_pressed_callback(tab_button_pressed_callback)
+
+        align_btn = menu.root.find_node("AlignButton", True).get_content()
+        align_btn.register_pressed_callback(align_button_pressed_callback)
+        align_btn.selected = True
+
+        run_button = menu.root.find_node("RunButton", True).get_content()
+        run_button.register_pressed_callback(run_button_pressed_callback)
+        self._run_button = run_button
+
+        # lists
+        self._complex_list = menu.root.find_node("ComplexList", True).get_content()
+        self._receptor_tab = menu.root.find_node("ReceptorButton", True).get_content()
+        self._ligand_tab = menu.root.find_node("LigandButton", True).get_content()
+        self._site_tab = menu.root.find_node("SiteButton", True).get_content()
+
+        # Update the menu
+        self._menu = menu
+        self._plugin.update_menu(menu)
+        nanome.util.Logs.debug("Constructed plugin menu")
diff --git a/nanome_docking/_docking_menu.json b/nanome_docking/_docking_menu.json
index f47aeb9..bd8feec 100644
--- a/nanome_docking/_docking_menu.json
+++ b/nanome_docking/_docking_menu.json
@@ -1 +1 @@
-{"title": "Docking", "version": 0, "width": 0.829999983310699, "height": 0.600000023841858, "is_menu": true, "effective_root": {"name": "Root", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 1, "forward_dist": 0, "padding_type": 1, "padding_x": -1, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "", "text_vertical_align": 1, "text_horizontal_align": 1, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 1, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": [{"name": "LeftSideScore", "enabled": false, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "ScoreList", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 5, "forward_dist": 0.01, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"display_columns": 1, "display_rows": 6, "total_columns": 1, "unusable": false, "type_name": "List"}, "children": []}, {"name": "CloseScoreButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0.0179999992251396, "padding_z": 0.0149999996647239, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "--", "text_value_selected": "--", "text_value_highlighted": "--", "text_value_selected_highlighted": "--", "text_value_unusable": "--", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 1, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "LeftSide", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Top", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 2, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "RecepeterData", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "ReceptorIcon", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.119999997317791, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0.00999999977648258, "padding_z": 0.00999999977648258, "padding_w": 0.00999999977648258, "content": null, "children": []}, {"name": "ReceptorText", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Receptor:", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}]}, {"name": "LigandData", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "LigandIcon", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 0.119999997317791, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0.00999999977648258, "padding_z": 0.00999999977648258, "padding_w": 0.00999999977648258, "content": null, "children": []}, {"name": "LigandText", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Ligand:", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}]}, {"name": "SiteData", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "SiteIcon", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.119999997317791, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0.00999999977648258, "padding_z": 0.00999999977648258, "padding_w": 0.00999999977648258, "content": null, "children": []}, {"name": "SiteText", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Site:", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}]}]}, {"name": "Bot", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 4, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Tabs", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 0.270000010728836, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Receptor", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "ReceptorButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Receptor", "text_value_selected": "Receptor", "text_value_highlighted": "Receptor", "text_value_selected_highlighted": "Receptor", "text_value_unusable": "Receptor", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.280000001192093, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "Ligand", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "LigandButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Ligand", "text_value_selected": "Ligand", "text_value_highlighted": "Ligand", "text_value_selected_highlighted": "Ligand", "text_value_unusable": "Ligand", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "Site", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "SiteButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Site", "text_value_selected": "Site", "text_value_highlighted": "Site", "text_value_selected_highlighted": "Site", "text_value_unusable": "Site", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}]}, {"name": "List", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0.01, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Mesh", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"mesh_color": 691685119, "type_name": "Mesh"}, "children": []}, {"name": "ComplexList", "enabled": true, "layer": 1, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0.01, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"display_columns": 1, "display_rows": 3, "total_columns": 1, "unusable": false, "type_name": "List"}, "children": []}]}]}]}, {"name": "RightSide", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.75, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Exhaustiveness", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Exhaust.", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "ExhaustivenessInput", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 10, "placeholder_text": "10", "input_text": "10", "type_name": "Text Input"}, "children": []}]}, {"name": "NumModes", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Num Modes", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "ModesInput", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 5, "placeholder_text": "5", "input_text": "5", "type_name": "Text Input"}, "children": []}]}, {"name": "Autobox", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Autobox", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "AutoboxInput", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 4, "placeholder_text": "4", "input_text": "4", "type_name": "Text Input"}, "children": []}]}, {"name": "AlignAfter", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, 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"text_value_idle": "Run", "text_value_selected": "Run", "text_value_highlighted": "Run", "text_value_selected_highlighted": "Run", "text_value_unusable": "Running...", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.430000007152557, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}]}]}}
\ No newline at end of file
diff --git a/nanome_docking/_docking_menu_rhodium.json b/nanome_docking/_docking_menu_rhodium.json
new file mode 100644
index 0000000..c837eb2
--- /dev/null
+++ b/nanome_docking/_docking_menu_rhodium.json
@@ -0,0 +1 @@
+{"title": "Docking", "version": 0, "width": 0.829999983310699, "height": 0.600000023841858, "is_menu": true, "effective_root": {"name": "Root", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 1, "forward_dist": 0, "padding_type": 1, "padding_x": -1, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "", "text_vertical_align": 1, "text_horizontal_align": 1, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 1, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": [{"name": "LeftSide", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Top", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 2, "forward_dist": 0, 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"padding_w": 0, "content": {"text": "Ligand:", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}]}, {"name": "SiteData", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "SiteIcon", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 0.119999997317791, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0.00999999977648258, "padding_z": 0.00999999977648258, "padding_w": 0.00999999977648258, "content": null, "children": []}, {"name": "SiteText", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, 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"padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "LigandButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Ligand", "text_value_selected": "Ligand", "text_value_highlighted": "Ligand", "text_value_selected_highlighted": "Ligand", "text_value_unusable": "Ligand", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "Site", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "SiteButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Site", "text_value_selected": "Site", "text_value_highlighted": "Site", "text_value_selected_highlighted": "Site", "text_value_unusable": "Site", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.300000011920929, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}]}, {"name": "List", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0.00999999977648258, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Mesh", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"mesh_color": 691685119, "type_name": "Mesh"}, "children": []}, {"name": "ComplexList", "enabled": true, "layer": 1, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0.00999999977648258, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"display_columns": 1, "display_rows": 3, "total_columns": 1, "unusable": false, "type_name": "List"}, "children": []}]}]}]}, {"name": "RightSide", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.75, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "GridResolution", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Grid Res.", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "GridResolutionInput", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 5, "placeholder_text": "2.5", "input_text": "2.5", "type_name": "Text Input"}, "children": []}]}, {"name": "PosesCount", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Poses ct.", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "PosesCountInput", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 3, "placeholder_text": "128", "input_text": "128", "type_name": "Text Input"}, "children": []}]}, {"name": "RotamerCount", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Rotamer ct.", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "RotamerCountInput", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0.0020000000949949, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"max_length": 2, "placeholder_text": "6", "input_text": "6", "type_name": "Text Input"}, "children": []}]}, {"name": "AlignAfter", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Align After", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.349999994039536, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "AlignButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "off", "text_value_selected": "on", "text_value_highlighted": "off", "text_value_selected_highlighted": "on", "text_value_unusable": "off", "text_auto_size": true, "text_min_size": 0, "text_max_size": 72, "text_size": 1, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "IgnoreHet", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "Text", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": {"text": "Ignore Het.", "text_vertical_align": 1, "text_horizontal_align": 0, "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.330000013113022, "text_color": -1, "text_bold": true, "text_italics": false, "text_underlined": false, "type_name": "Label"}, "children": []}, {"name": "IgnoreHetButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 0.400000005960464, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0.0149999996647239, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "off", "text_value_selected": "on", "text_value_highlighted": "off", "text_value_selected_highlighted": "on", "text_value_unusable": "off", "text_auto_size": true, "text_min_size": 0, "text_max_size": 72, "text_size": 1, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "Run", "enabled": true, "layer": 0, "layout_orientation": 1, "sizing_type": 2, "sizing_value": 1, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": [{"name": "RunButton", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0.0179999992251396, "padding_y": 0, "padding_z": 0.0149999996647239, "padding_w": 0, "content": {"selected": false, "unusable": false, "text_active": true, "text_value_idle": "Run", "text_value_selected": "Run", "text_value_highlighted": "Run", "text_value_selected_highlighted": "Run", "text_value_unusable": "Running...", "text_auto_size": false, "text_min_size": 0, "text_max_size": 72, "text_size": 0.430000007152557, "text_underlined": false, "text_bolded": true, "text_vertical_align": 1, "text_horizontal_align": 1, "type_name": "Button"}, "children": []}]}, {"name": "Logo", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 2, "sizing_value": 1.5, "forward_dist": 0, "padding_type": 0, "padding_x": 0.01, "padding_y": 0, "padding_z": 0.01, "padding_w": 0, "content": null, "children": [{"name": "LogoImage", "enabled": true, "layer": 0, "layout_orientation": 0, "sizing_type": 0, "sizing_value": 0, "forward_dist": 0, "padding_type": 0, "padding_x": 0, "padding_y": 0, "padding_z": 0, "padding_w": 0, "content": null, "children": []}]}]}]}}
\ No newline at end of file
diff --git a/nanome_docking/swri_logo.png b/nanome_docking/swri_logo.png
new file mode 100644
index 0000000..4ecbbc1
Binary files /dev/null and b/nanome_docking/swri_logo.png differ
diff --git a/publish.sh b/publish.sh
old mode 100644
new mode 100755
diff --git a/setup.py b/setup.py
index eddccc2..79b4f8e 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,13 @@
-import pathlib
+import os
 from setuptools import find_packages, setup
 
-README = (pathlib.Path(__file__).parent / "README.md").read_text()
+with open(os.path.join(os.path.dirname(__file__), "README.md"), 'r') as file:
+	README = file.read()
 
 setup(
 	name = 'nanome-docking',
 	packages=find_packages(),
-	version = '0.1.4',
+	version = '0.1.5',
 	license='MIT',
 	description = 'Nanome Plugin to dock ligands to a receptor',
 	long_description = README,