Introduction

The structure tab launches Mol*, a web-based 3D visualization tool that can be used without downloading or installing software or apps.

Why use the Structure tab?

Mol* enables users to display all or selectively display parts of a structure, change molecular representations, and color them in meaningful ways to examine, explore, measure, and compare molecular structures. The tool also allows analysis of interactions throughout the structure or in the neighborhood of a single residue or ligand and exploration of sequence and structural motifs. Mol* images of all or parts of the structure can be captured for publication, communication, and discussion.

Documentation

The interface

Mol*, as used in the Structure tab, simultaneously displays the molecules in the structure in 3D and the sequences of polymers present in the structure, along with ligands, ions, water molecules, etc. (Figure 1).

Figure 1: The 3D interactive view of T4 Lysozyme, PDB ID pdb_0000102l, showing the 3D Canvas, Sequence, and Controls panels.

• The 3D canvas is where the molecule is displayed. Moving the mouse in this region of the screen moves (rotate, translate, and zoom into) the structure.
• The sequence panel is marked with a horizontal box with a red outline. This can be used to click on any one or a group of amino acids to center on them and zoom in to see the non-covalent interactions.
• The Controls panel provides options to display, hide, change representations, and color the polymer chains and/or ligands.
• Learn more from the Mol* Documentation.

Learning about the Structure

Here are a few things that you can learn about the structure from visualizing a biomolecular structure in Mol*.

• Polymer chains: The T4 lysozyme structure shown in Figure 1 has a single protein chain (colored green). The first polymer chain in an entry is usually colored green. Other polymers in the entry are colored in different colors for easy identification and analysis.
• Ligands: The ligand BME, water molecules, and ions are displayed in the ball-and-stick representation and colored according to the CPK color scheme. Only the carbon atoms in the ligands are colored to match the chain ID with which the ligand is associated.
• Location and interactions between polymer and non-polymer entities: The pulldown menu on top of the sequence panel allows you to view any of these polymeric or non-polymeric entities in the sequence panel and select the instance from the list of chain and asym IDs. The components displayed in the Control panel also allow selection and changes in representation of all or specific parts of the structure.

Exploring other structures

The Structure tab opens a specific PDB entry in Mol*. However, more than one structure may be displayed in the tool in the following ways:

• The stand-alone Mol* tool allows you to upload multiple structures, either by specifying their PDB IDs or by uploading files by providing the complete paths for them. Learn more about how to compare and superpose (also referred to as superimpose) structures.
• Structures aligned using the pairwise alignment tool can be displayed in Mol*. Learn more about the pairwise structure alignment tool.