Menus

Selector Menu Basics

View/Sort Dropdown

This menu provides component specific dropdown options to change the list of items in the component menu space.

Expand/Collapse All Groups - This option is available in Compound, Fragments, and Protein dropdown menus. Subgroups may be expanded to see all sub-elements or collapsed to only see main group components. This is especially useful for protein chains and fragment sets.

Fragment Dropdown

Sort by [User vs Builtin Fragments, User Fragment Sets, Fragment Library] - These options allow the fragments to be sorted according to various libraries of fragments.

Hide all fragments - If fragments have been selected by clicking on a fragment in the fragment menu, then clicking the "Hide all fragments" option in the dropdown will hide the visible fragments. If no fragments are showing then this button will impart no visible change. Note, this button also does not impact fragments that have been added to the system via using a fragment query option in the right click menu of the main 3D structure viewing window.

Manage Fragments - This button opens the fragment manager window where fragments to be included in fragment queries can be reviewed and updated. More info on the fragment manager can be found in the Compound Design section.

Protein Dropdown

Sort by [Chain, Type] - This sorting will change the ordering of major sections. While Sort by Chain will order protein components according to their chains as indicated in the PDB, Sort by Type sorts by chemical components including Target, Ions, Crystal Water, Hot Spots, and more.

Add another protein (Selectivity) - This is one method to engage with the Selectivity Workflow. Selecting this button will bring up the protein select menu with the selectivity radio button pre-selected.

Clear workspace - This will remove all components from the workspace including compounds, fragments, and proteins.

Filter Components Text Box

This textbox permits the user to update what components are show in the Selector Menu tab that is currently selected.

Compounds

Pin

Pin off -

Pin on -

The pin button permits keeping multiple selections in the workspace. When the pin is on, the compound will remain in the workspace regardless of if you click on another compound in the Selector menu. 

It is crucially important to remember that the Inspector menu responds to the compounds currently in the workspace. If you wish to see multiple energies or properties side by side in the Inspector menu, then you must have all of those compounds pinned in the workspace. The currently focused compound will also always show up in the Inspector menu.

Ellipse Menu Options

In the compound tab, the ellipse dropdown menu is available for each imported compound. 

Edit - This brings up the compound in the 2D compound editor.

Minimize - Minimize the geometry of the compound.

Dock - Brings up the Docking Menu to permit docking the compound to a target in the workspace. More details can be found in the Docking Section.

Export - Brings up the export menu which allows exporting compound mol data, and image of the compound, as well as connections to many external integrations. More information can be found in the Export and External Integration Section.

PubChem Search - Specifically links to the PubChem external integration in the export menu.

Duplicate - This duplicates the compound giving it a new name similar to the original name but with a suffix of _#.

Create New Group - Creates a new group in the compound tab. This does not automatically put the compound from which the new group was created into the new group, so it and any other compounds to be added to the group must be dragged to the group name to become group members. The drag and drop group feature is only available for user created compound groups.

Focus/Zoom

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The arrow to the right of each compound is the focus button. This button updates what compound is shown in the workspace. Note that pins will keep all pinned compounds visible. A focused compound will have its button change into the zoom button. This zoom button may then be used to toggle between ligand and protein views which are discussed more in the Visualization Section.

Right Click

Right clicking an unselected compound (selection is noted by a highlighted color change) will give the option to delete the right-clicked compound or rename it in addition to the ellipse dropdown menu options.

Right clicking a selected compound (selection is noted by a highlighted color change and is performed by a left click or shift left click) will give the option to delete the right-clicked selected compounds or group the selected compounds, in addition to the ellipse dropdown menu items. Note that selecting multiple compounds at once can allow you to perform group actions like requesting minimization on multiple molecules at once.

Group Ellipse Dropdown Menu

The Group Ellipse Dropdown Menu allows the single compound ellipse dropdown actions to be performed on an entire group. There are also options unique to this menu.

Rename Group - Renames the group name, not the compound names.

Delete Group - Deletes the grouping element "parent" and "children" compounds that are not part of an imported protein description.

Sort this group by Interaction Score - This sorts the compounds by interaction score with the target (more negative to the top). Note that if the compound has not had an interaction score calculated yet it will be moved to the bottom of the list.

Sort this group alphabetically - This sorts the compounds alphabetically by their name.

Ungroup - This will ungroup the grouped compounds and return them to individual compounds.

Info Button

The info button will show the 2D depiction of the compound as well as the derivation pathway from which the compound was generated.

Fragments/Proteins

Show

Show off - 

Show on - 

Show can be selected for every fragment/protein individually or via selecting a group show button. Shown fragments will show the fragments that have been sampled via a fragment query. All pre-loaded proteins already have had the fragment query run for the internal BMaps Fragments sets and water maps. Many proteins also have Hotspots that can be shown in the protein tab.

Fragments

Fragments and water maps are visualizable and manipulated from this menu.

Ellipse Menu Options

Hide all fragments - Hides all fragments in the visualized in the workspace.

Hide all but this fragment - Hides all fragments except the fragment whose ellipse was clicked.

Hide all fragments not in this group - Hides all fragments not in the group whose ellipse was clicked.

Fragment Energy Filter

The fragment energy filter will be displayed at the bottom of the fragments tab for the currently selected fragment, or, if multiple fragments are selected, the top selected fragment will be used in the energy filter box. This fragment energy corresponds to the free energy of the fragment simulation at which the displayed fragments were found. Using the white circle slider to adjust the threshold will show which fragments were more or less favorable during the simulation with respect to the target. Note that we do not include positive free energies here because that would suggest the fragment could not be present in a stable state without additional application of energy not displayed in the system environment.

Info Button

The info button will show the 2D depiction of the fragment.

Proteins

Ellipse Menu Options

Hide this component - Hide this component from the 3D workspace.

Select 3D atoms - Selects the atoms corresponding to the component whose ellipse was clicked in the 3D workspace. Selection shows as the elements becoming pink.

Groups elements may all be hidden and shown via the group ellipse dropdown.

Hotspots may be shown or hidden individually or as a group. More info on Hotspots available in the Hit Determination Section.

Hotspot Average Energy Filter

When the hotspots are visualized in the 3D workspace, the average energy filter will act as a threshold for showing and hiding hotspots based on the average energy of the hotspot. The average energy is determined based on the energy of fragments found at that hotspot. The average excess chemical potential for a hotspot can be viewed in the associated info button.

Inspector Menu Basics

The Inspector menu provides the user with insights both qualitative and quantitative about the compound with respect to the protein. Multiple compounds may be described at once, side-by-side. The compounds described are determined by which compounds are active in the workspace. This may be changed either for one compound by changing the focus using the arrow to the right of the compound. Or else multiple compounds may be added to the workspace at once using the pin to the left of each compound.

Should the tabs ever show the message "No compounds available" you will need to refocus or pin a compound in the Compounds Selector menu.

Structure

The 2D depiction of the currently focused compound.

Energies

The energies of the currently focused and pinned compounds. Compounds that have not already had energies calculated can have energies calculated by clicking the Calculate button under their name.

Properties

The properties of the currently focused and pinned compounds.

Properties currently available are Molecular Weight (Mol. Weight), LogP, Energy Efficiency, PSA (Polar Surface Area), # Heavy Atoms (Non-hydrogen), Charge, HB (Hydrogen Bonding) Donors/Acceptors, # of Rotatable Bonds (# Rot. Bonds)

Ligand Interaction Diagram (LID)

The ligand interaction diagram is shown for the focused compound. The interactions between the ligand and the target are highlighted in a 2D diagram, where the labels can be moved around by dragging. Different types of interactions are color coded according to the labels at the bottom of the LID. Each label may be clicked to hide or show all interactions of that type. The LID comes from the paper: "ProLIF" ligand interaction diagram from ChemoSim Lab.