# Navigating Nanome
The Nanome Lobby is where users can sign into an account or sign up. By toggling the 'Remember Me' button, users can automatically be signed in the next time they start Nanome. Users can also start the tutorial by selecting 'Start Tutorial'.
# Creating an Account
An email address is required to create a Nanome account.
Terms & Conditions: https://nanome.ai/terms/
The tutorial consists of 19 levels. Follow the instructions on the Level Panel and the narrated audio to complete the levels.
# Navigating the Tutorial Using Level Panels
Users can visit previous levels by selecting the 'back' button on the Level Panel. Users can skip the current tutorial level by selecting the 'Skip' button on the Level Panel.
Users can restart the level by selecting the refresh icon on the left of the Level Panel once a level is complete. Users can move onto the next level by selecting the right arrow on the right of the Level Panel once a level is complete.
# Bar Buttons
Refresh, Creating a Room, and Settings
Users can refresh the available room list by selecting the 'Refresh' button at the top of the Lobby Navigation Bar Buttons.
# Creating a Room
There are three Room Types a user can create depending on their Nanome License.
- Public Rooms: Anyone can join in the room. available to all Nanome licenses
- Private Rooms: A password is set for the room. Available to Academic and Enterprise
- Single User: Offline mode which no one else can join. Available to Academic and Enterprise
In the Setting tab, users can adjust various settings.
- Configuration Viewer
By selecting the Configuration button in the Setting tab, users can view the Nanome Configuration file, which contains additional settings that cannot be controlled directly from within the app. The Configuration file can be located in the same directory as the app build directory.
# Bar Statuses
# Server Type
Indicates connection to Nanome Public Server or Custom Private Server
Indicates Nanome version
# Update Banner
The update banner features the latest features that are added in the build that the users are in.
# Joining a Room
In order to join a room, select a room from the lobby.
In addition to physically moving around in VR, users can teleport around the environment by pointing to a spot on the floor and clicking and holding with their index finger.
# Environment Scaling
In order to scale the environment or molecular structures, press down on the middle finger 'grip' button on each controller. Next, bring the controllers together to scale the environment smaller or pull them apart to scale the environment larger.
# Structure Grabbing & Moving
In order to grab a structure, reach out and press the middle finger 'grip' button on one of the left or right controllers. Users can also grab structures from a distance by pointing their ray/laser and then pressing the 'grip' button.
Once the structure is grabbed, users can use the joystick or touchpad of their controllers to move the structure closer or further away from them.
# Entry Menu Grabbing & Scaling
The Load, Plugin, Display, Color, Modify, Select, and Macro Menus can be displayed by clicking their respective icons located at the bottom of the Entry Menu.
# Entry List
The Entry List is a list of all of the structures that have been loaded into the environment.
# Hierarchy Buttons
Hierarchy buttons can be used to navigate the structure's substructures such as chains and residues.
# Different Viewing Modes (Small, Medium, Large)
Different Viewing Modes can be toggled to modify the substructure icon sizes in each menu.
# Frame Data
Frame data allows users to navigate and modify different frames of the same structure (Academic and Enterprise only).
# Electron Density Maps
The Electron Density tab shows the configuration of viewing the Electron Density Map of the structure (Academic and Enterprise only).
# Select/Deselect All
Select or deselect all present structures.
# Invert Selection
Invert current selection.
# Toggle Lock
Lock or unlock selected entities.
# Toggle Box
Show or hide the box frame of selected entities.
# Toggle Visibility
Show or hide the selected entities.
Save the current workspace.
# New Workspace
Discard the current workspace and create a new one.
Export the selected structures in a generic format.
Align the selected entities and place them in the same position under the same coordinate system. Caution: this does not necessarily align the entities by their atom position, and the entities could end up not overlapping after the alignment.
Delete the selected entities.
Load molecules or structures into your workspace. Supported file formats include: .pdb, .cif, .mmcif, .sdf, .mol, .xyz, .mol2, .ccp4, .dsn6, .pse, .nanome, .png, .jpg, .jpeg, .pdf
Molecules featured by Nanome for their interesting properties or background.
From the Database tab, structures can be directly loaded from RCSB, DrugBank (Academic and Enterprise only), or PubChem (Academic and Enterprise only). Custom database can also be added by changing the config file.
From the Keyword tab, structure can be loaded from a keyword search.
# My Files
My Files tab allows users to load structures from their local directory.
Recent files loaded in Nanome.
This tab contains options for the visual of atoms and bonds.
Hide atoms and show bonds in thin wire visual.
Show small atoms and bonds in volumetric stick visual.
- Van Der Waals
Show atoms in thin Van Der Waals visual and hide bonds.
Show atoms with radius proportion to their b-factor value and hide bonds.
- Ball & Stick
- Hide all atoms and bonds.
This tab contains options for the visual of ribbons.
Show ribbon in cartoon visual that highlight secondary structures using helix and arrows.
Show ribbon in uniform tube visual.
Show ribbon in tube with widths proportion to the atoms' b-factor value.
- Show Surface
Show the solvent-excluded-surface.
Change the opacity of the surface.
# Sub Structure
Hide hetatoms, waters and hydrogen.
Show hetatoms, including water.
Show labels on atoms.
Show labels on residues.
Apply a solid color or a color scheme on the selected structures.
Colors picked in picker are applied in a solid style.
Carbonite color applies only to carbons.
Monochrome color applies to all atoms indifferently.
Colors picked in schemes are applied in a certain pattern.
- YRB Hydrophobe
Color selected structures by their hydrophobicity with yellow, red, blue colors.
Other available color schemes include coloring by occupancy, b-factor, rainbow and so on.
Edit the selected structures by applying actions from the buttons.
Apply certain computations on the selected structures and modify them according to the result.
- Calculate Hbond
Config the threshold for generating h-bonds.
Config forcefield and step for minimizing potential energy of selected structures.
Switch to a certain tool to directly apply modification to the structures.
Mutate the R-groups of the selected amino acids.
Quickly modify selection range using certain criteria.
Refine selection by applying certain changes.
- Replace Selection
# Atom Type
Select or deselect certain types of atoms.
# Residue Type
Select or deselect certain types of residues.
Expand or shrink the selection range by physical proximity.
# Wrist Menus
Wrist menu contains access to features independent from the content of the workspace such as quick menu access, room management.
# Quick Menus
Toggle on and off each menu quickly or all at once.
- Manage Users
Manage users by giving them the presenter privilage or teleporting them.
- Presenter Requests
View the presenter requests and grant presenter privilege.
# Menu Layouts
Quickly manage the enabled menus and format them in certain layouts.
Change settings such as volumes and environment background.
# Context / Action Menu
# Tools Menu
Press and hold the menu button to activate the tool selection menu, hover over the desired selection and then release the button. If no selection is made, the hand tool will be chosen by default. If you are using a Vive system, press and hold the touch pad on your right controller to activate the menu. If you are using an Oculus system, press and hold the B button on your right controller to activate the menu.
# Hand Tool
The Hand Tool is the default state of the hand and allows for basic interaction including grabbing and clicking.
# Measurement Tool
Measurement Tool places measurement points and measure the distances and angles between atoms and points of interests.
# Selection Tool
Selection Tool selects structures directly in the workspace.
# Torsion Tool
Torsion Tool twists rotatable bonds and changes the dihedral angles between atoms.
# MedChem Tools
MedChem Tools enable editing the atoms directly using hands, bundling a rich set of features including atom addition and removal.
Offers options to quickly access binding sites and config the auxiliary features such as auto-minimization.
Select a substructure from the build menu and build it on top of existing atoms using MedChem Tool.
# Periodic Table
Select any atom type from the periodic table to use in build mode.
# 2D UI
Nanome is accessible from a keyboard and mouse setup on a 2D monitor as well.
Manage users or request presenter privilege.
# Menu Management
Toggle or manage menus.
# View Navigation
Change options for view control.
Change settings including volume and environment background.
The control scheme can be accessed at any time by pressing the [H] key on the keyboard.