Maneuvering in Mol*

Depending on what you wish to view in Mol* and how you wish to interact with the molecule(s) visualized in the 3D canvas, Mol* offers a few different modes and specific logic to perform the desired actions. This section is aimed at explaining the fundamentals of how Mol* works and how to effectively perform actions within it.

Deciding what to visualize

• For any structure of interest, the Mol* tool can be used to view the entire molecule (or model), specifically selected subsets of it, or supersets (assemblies) of the structure.
• The choice for what to visualize in the 3D canvas can be made using the Structure Panel options in the Controls panel. Learn about the Preset options available.
• It is important to select and view the deposited coordinates, biological assembly, single model, ensemble etc. in order to meet the needs of the planned exploration.

Examples: A few examples illustrate options in the Structure panel to customize the molecular display in the 3D canvas. Different assemblies of the X-ray structure of insulin are shown in Figure 1. Note that each polymer chain is colored in a different color. The representative model and ensemble of the NMR structure of proinsulin is shown in Figure 2. Various assemblies of proteins making up the X-ray structure of satellite tobacco mosaic virus, an icosahedral virus, are shown in Figure 3. The model and assembly coordinates are identical for CSMs - in the default view, CSMs with a single polymer chain are colored by residue-level pLDDT scores in the 3D canvas. The same structure in the assembly view and CSMs with more than one polymer are displayed with different colors for each polymer chain (Figure 4).

Figure 1: A sampling of molecular views displayed on the 3D canvas for a single structure (PDB entry 1trz). A. view of the entire set of coordinates included in the PDB entry; B. a subset of the structure corresponding to a biological assembly; C. display of the contents of the Unit cell for the specific structure; D. A superset of the coordinates in the PDB entry, representing an alternate biological assembly. The additional coordinates were computed based on crystallography symmetry information.

Figure 2: Different molecular views of a single structure determined by NMR (PDB ID 2kqp). A. a single model (from the deposited coordinates); B. The full ensemble of NMR structures.

Figure 3: A sampling of molecular views displayed on the 3D canvas for an icosahedral virus structure (PDB entry 1a34). A. the complete icosahedral assembly showing the full virus structure; B. view of the entire set of coordinates included in the PDB entry representing one icosahedral unit of the complete virus (1/60th of the structure); C. a subset of the icosahedral virus, forming a pentamer; D. a subset of the icosahedral virus, forming a trimer. The additional coordinates were computed based on icosahedral symmetry information.

Figure 4: Viewing CSMs in Mol* - A. default view of the AlphaFold model AF_AFA0A023FBW7F1 showing residue level pLDDT (model confidence) scores; B. Assembly view of the AlphaFold model AF_AFA0A023FBW7F1 ; and C. Model Archive model MA_MABAKCEPC0003.

Interacting with the Molecule(s)

Once the desired molecule(s)/assembly(ies) are displayed on the 3D canvas you can interact with the molecule to examine it closely, select parts of the molecule to color, change representations, hide, label, measure etc.; and save selections in the form of components to view and analyze independent of the rest of the structure.

Focus

Focusing adjusts the view of the camera and the center of rotation on specific atoms, residues, or parts of structures. Once the camera is focused on a selection, other items in the structure may appear hidden from the camera because they fall outside the region being viewed or are clipped.

There are three ways to change the focus of the camera:

• Click on a residue in the 3D canvas or in the Sequence Panel - In default mode, click on a residue to automatically center on it, zoom-in, and display it in ball and stick representation along with its surrounding residues. A temporary component called “[Focus] Target” is created for the residue being examined. Another temporary component called “[Focus] Surroundings (5 Å)” is created for all the surrounding residues and appears below existing components in the Components panel. All local non-covalent interactions between these residues are also shown. (see Figure 5A)
• Click on an existing component - If a component is already listed in the Components Panel, it can be clicked on which will make it the focus of the camera. (See Figure 5B)
• Click on selected objects - If an object is currently selected, it will be listed in the Structure Panel. For example, if four residues are selected, the Structure Panel will read “4 Residues Selected.” If this text is clicked on, the four residues will become the focus. (See Figure 5C).

Figure 5: Different ways of focusing on A. a specific residue; B. existing component; C. selected residues.

Selections Logic

Making selections is often the first step to performing a range of operations. Selections are made using Selection Mode which is activated using the cursor or arrow head icon in the Toggle Menu. The Picking Level determines the specificity of the selection. For example, keeping the Picking Level on “residue” enables individual or groups of amino acid residues to be selected, while changing the Picking Level to “chain” allows whole chains to be selected. After the desired Picking Level is chosen, selections can be made by:

• Clicking on parts of the structure in the 3D canvas
• Clicking on residues in the Sequence Panel
• Using the Set Operations Menus in Selection Mode toolbar

After selections are made, several tasks can be directly performed using the current selection. These include:

• Creating a component of the current selection
• Coloring the current selection
• Changing the transparency of the current selection
• Changing the representation of the current selection (e.g., ball & stick, molecular surface)
• Removing the current selection from the 3D canvas
• Focusing on the current selection
• Creating labels and measurements

Components Logic

After making a selection, a component can be made from it. Creating components allows the user to make groupings of certain parts of a structure which can later be manipulated. It is not always necessary to create components, but it can be helpful in certain circumstances. For example, if you have selected a number of residues in a protein that you may be returning to multiple times to perform different actions, it may be helpful to create a component for quick reference.

The following are actions that can be performed with components:

• Showing/hiding using the eye icon
• Changing the representation
• Coloring by various requirements
• Modifying the component to add, subtract, or intersect pieces of the structure in the selection
• Deleting the component - this will remove the grouping of selected parts of the structure but the structure will remain intact

Once again, it is not always required to make components, but can be useful for easy reference. Clicking on a component in the Components Panel will quickly focus on that component in the 3D canvas. Additionally, the component can be easily selected from the Components Panel.

Using a component can be helpful for certain tasks:

• Briefly hiding a group to view another part of the structure
• Coloring a selection with specific settings
• Changing the representation after hiding certain parts of the structure
• Grouping certain parts of different components into other components by modifying selection