# 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.
# 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).
# 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 Configuration
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
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.
# Plugin
Please view the plug in page to learn more.
# Display
# Atom
This tab contains options for the visual of atoms and bonds.
- 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.
- 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
- Show Surface
Show the solvent-excluded-surface.
- Opacity
Change the opacity of the surface.
# Sub Structure
- None
Hide hetatoms, waters and hydrogen.
- Hetatoms
Show hetatoms.
- Waters
Show hetatoms, including water.
- Hydrogens
Show hydrogens.
# Labels
- Atoms
Show labels on atoms.
- Residue
Show labels on residues.
- Chain
Show labels on Chains. (Coming Soon)
# Color
Apply a solid color or a color scheme on the selected structures.
# Picker
Colors picked in picker are applied in a solid style.
- 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.
- Monochrome
- Carbonite
- 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.
# 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
