# Main Menus

# Entry List

The Entry List is a list of all of the structures that have been loaded into the environment.

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 List.

# Quest Limiter

The Quest Limiter is an indicator that shows how close the current amount of atoms is to hitting the limit of Quest's computing capability. This indicator only shows up in the Quest version of Nanome software. When the amount of atoms approaches or hit the limit, the following prompts will show up.

# Hierarchy Menu

Hierarchy menus lists out the component of an entity, such as chains and residues, in hierarchical levels.

# Different Browsing 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).

# Menu Actions

Action buttons on the Entry List provide quick access to common actions on the workspace.

Action	Description	Additional Menu
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	Save the current workspace.
New Workspace	Discard the current workspace and create a new one.
Export	Export the selected structures in a desired format.
Align	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.
Sequence	View the seqences of multiple chains and align them.
Delete	Delete the selected entities.

# Load

Load molecules or structures into your workspace. Supported file formats include: .pdb, .cif, .mmcif, .sdf, .mol, .xyz, .mol2, .ccp4, .dsn6, .dcd, .gro, .pqr, .trr, .xtc, .psf, .pse, .nanome, .png, .jpg, .jpeg, .pdf

# Featured

Workspaces that contain featured structures and tutorials.

Molecules featured by Nanome for their interesting properties or background.

# Database

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.

# Keyword

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

Recent files loaded in Nanome.

# Stacks

Please view the Nanome Stacks page to learn more.

# Display

# Atom

This tab contains options for the visual of atoms and bonds.

Option	Description	Fig.
Wire	Hide atoms and show bonds in thin wire visual.
Stick	Show small atoms and bonds in volumetric stick visual.
Van Der Waals	Show atoms in thin Van Der Waals visual and hide bonds.
Adaptive	Show atoms with radius proportion to their color value and hide bonds.
Ball & Stick	Hide all atoms and bonds.

# Ribbon

This tab contains options for the visual of ribbons.

Visual	Description	Fig.
Cartoon	Show ribbon in cartoon visual that highlight secondary structures using helix and arrows.
Coil	Show ribbon in uniform tube visual.
Putty	Show ribbon in tube with widths proportion to the atoms' color value.

# Surface

Toggle the visibility of solvent-excluded-surface or change its opacity.

# Sub Structure

Option	Description	Fig.
Hetatoms	Show hetatoms.
Waters	Show hetatoms, including water.
Hydrogens	Show hydrogens.

# Labels

Option	Description	Fig.
Atoms	Show labels on atoms.
Residue	Show labels on residues.

# Color

Apply a solid color or a color scheme on the selected structures.

# Picker

Colors picked in picker are applied in a solid style.

Option	Description	Fig.
Carbonite	Carbonite color applies only to carbons.
Monochrome	Monochrome color applies to all atoms indifferently.

# Schemes

Colors picked in schemes are applied in a certain pattern.

• YRB Hydrophobe

Color selected structures by their hydrophobicity with yellow, red, blue colors.

• IMGT

Color selected antibody structures by their regions.

Other available color schemes include coloring by occupancy, b-factor, rainbow and so on.

# Modify

# Edit

Edit the selected structures by applying actions from the buttons.

# Compute

Apply certain computations on the selected structures and modify them according to the result.

• Calculate ESP

Generate the Electron Potential Map of the selected structure.

• Calculate Clashes

Config the tolerance of atom clashes.

• Calculate Hbond

Config the threshold for generating h-bonds.

• Minimize

Config forcefield and step for minimizing potential energy of selected structures.

# Tools

Switch to a certain tool to directly apply modification to the structures.

# Mutate

Mutate the R-groups of the selected amino acids.

# Select

Quickly modify selection range using certain criteria.

# Refine

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.

# Distance

Expand or shrink the selection range by physical proximity.

# Macro

Please view the macros page to learn more.