RCSB PDB Help

NGL to Mol* UI Migration Guide

○ Common Actions for Structure Displayed

The visualization tool NGL, is no longer available as a molecular viewer option from RCSB.org Structure Summary Pages (Structure tab). Learn more about this.

We recommend that you use Mol* for 3D visualization. Learn how to perform common NGL functions in Mol* in the following sections.

Structure View

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

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.

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

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.