3D Viewers

NGL to Mol* UI Migration Guide

Structure View

Figure 1: NGL interface showing Structure View options
Figure 1: NGL interface showing Structure View options
NGL Button/Options Function performed Equivalent function in Mol*
Assembly View structure as asymmetric unit, biological assembly, unit cell, or supercell (stacked unit cells) Switch between different models and biological assemblies for display in the 3D canvas
Model View specific model for multi-model structure Select specific models from an ensemble
Symmetry View intrinsic molecular symmetry. View molecular symmetry using the assembly symmetry panel
Style View the structure in different representation styles (Backbone, Surface, Cartoon, Spacefill/CPK, Licorice, Line, and Ball & Stick) Change representation of the structure
Color Color the structure using different color schemes e.g., By Chain, Element/CPK, Rainbow, Secondary Structure etc. Steps to color all or parts of the structure by chain, element/CPK, rainbow/spectrum color scheme, secondary structure etc.
Ligand Change the ligand representation style -- ligands can be displayed as ball-and-stick, space fill or turned off Change representation of the structure
Quality Adjust the rendering quality. When creating screenshots, set this option to 'high' for the best results Select appropriate resolution when taking screenshots.
Water Show or hide water molecules present in the structure Select specific parts of a structure to show or hide it
Ions Show or hide ions present in the structure Select specific parts of a structure to show or hide it
Hydrogens Show or hide hydrogen atoms included in the structure Show or hide hydrogen atoms
Clashes Show or hide clashes between atoms (indicated by pink disks) as given in the Validation Report View structure quality using the quality assessment panel

Electron Density Maps

Figure 2: NGL interface showing Electron Density Maps options
Figure 2: NGL interface showing Electron Density Maps options
NGL Button/Options Function performed Equivalent function in Mol*
Map Select and turn on the map(s) displayed - 2fo-fc map (colored blue), fo-fc map (negative density is colored red and positive peaks are colored green) Display the Electron Density map by activating the Density Panel.
Scroll Select the map whose isodensity level value will be changed with the mouse via "Ctrl scroll-wheel" The 2Fo-Fc and Fo-Fc level sliders in the Density Panel.
Level The value at which the isosurface of the map is shown (in sigma values). This value can be adjusted using the sliders for each map type or using the mouse via "Ctrl scroll-wheel" The 2Fo-Fc and Fo-Fc level sliders in the Density Panel.
Map Style Select the map display style (mesh, smooth, or flat) The default option for displaying the electron density map corresponds to the Smooth style. The wireframe option is equivalent to the mesh style (see Density Panel).
Map Size For efficiency, only a portion of the map is displayed. The map size option adjusts the size (in Å along each of the three crystallographic axes) of this portion Activate the electron density display using options in the Density Panel and use the sliders to focus around a specific area.
Ligand Recenter the view around the selected ligand Click on the “Interactions and Density” button in the Small Molecules section, 3D interaction column to view the electron density map around the selected ligand and polymer chain.

Ligand View and Options

Figure 3: NGL interface showing Ligand View. The panel on the right shows the options that become available when a specific ligand is selected.
Figure 3: NGL interface showing Ligand View. The panel on the right shows the options that become available when a specific ligand is selected.
NGL Button/Options Function performed Equivalent function in Mol*
Ligand Select the ligand to display and view the ligand and interactions in its neighborhood. Display the interactions of a ligand with amino acids and ligands in its neighborhood.
Opacity Change the opacity of the ligand binding pocket Display the hydrophobicity on the surface of the ligand binding pocket Change the Opacity of the surface as needed
Near Clipping Adjust the clipping plane for the ligand binding pocket Use Clip Planes to slice through and refine the view being displayed
Radius Clipping Change the radius of the clipping sphere around the ligand binding pocket Currently a binding pocket of 5 Å can be displayed around a selected ligand or custom residue selection. Additional coding is needed to display binding pockets of a custom radius.
Color Color the pocket surface using different schemes (element/CPK, hydrophobicity, and B-factor) Once you have drawn the binding pocket surface, you can change the color of the surface by selecting appropriate Color options.
Interactions Show or hide various interactions (Hydrophobic Contacts, Hydrogen Bonds, Halogen Bonds, Metal Interactions, Pi Interactions) Select the types of non-covalent interactions displayed when viewing the interactions in the neighborhood of a selected amino acid or ligand.
Label Display or hide labels for the ligand and neighboring residues Label any atom, ligand, or residue (amino acid or nucleotide) selected
Polymer Display Show or hide the current polymer display Show or hide any atom, ligand, or residue (amino acid or nucleotide) selected

Common Actions for Structure Displayed

Figure 4: Options in NGL to manipulate the display of molecule(s) loaded in the tool
Figure 4: Options in NGL to manipulate the display of molecule(s) loaded in the tool
NGL Button/Options Function performed Equivalent function in Mol*
Spin Start/stop spinning the structure along Y-axis Use Keyboard Controls - e.g., key “i”
Center Reset molecule position See option button in the General Interface toggle menu in or use the Keyboard Controls - e.g., key “t”
Fullscreen Activate/disable fullscreen mode Use the Extend Viewport option in the General Interface toggle menu
Screenshot Download screenshot (at twice the displayed resolution) Take Screenshots to save images.
Camera Perspective or Orthographic Select Camera options
Background White or Black Change the Background color
Focus Slides to move far and near clipping planes towards the center Change the camera Focus and center of rotation on specific atoms, residues, or parts of structures.

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Last updated: 1/16/2024