What do you do when you visualize a structure?

When visualizing any biomolecular structure [experimental structures or Computed Structure Models (CSMs)] the following five actions are commonly performed:
1. View overall shape and composition (use default mode of Mol*)
2. Change representations of all or parts of the molecule (use default mode of Mol*)
3. Examine the neighborhood of one or more residue or ligand (use default mode of Mol*)
4. Select all or parts of the molecule to measure, color, label etc. (use selection mode of Mol*)
5. Customize and Save views (use options from vertical toggle menu in 3D canvas)

Each of these actions and their various options are described here.

View overall shape and composition

When a biomolecular 3D structure is loaded into Mol* the following can help view what the structure looks like and how many proteins, nucleic acids, ligands etc. are included in it.

• In the 3D canvas
• The mouse controls can be used to rotate, zoom in, and view the overall shape in the 3D canvas
• Polymers (proteins and nucleic acids) are shown in the cartoon representation, while small molecule ligands, cofactors, modified residues etc. are displayed in the ball and stick representation.
• Each polymer chain in the structure (with a unique chain identifier) is colored in a different color - indicating the composition of the structure (see example PDB ID 4hhb). Note, in some cases multiple chains in an assembly may be computed based on crystallography symmetry, in this case the symmetry related chains may have the same color (see example PDB ID 9dna). The symmetry related polymer chains can be colored in different colors by coloring them by instance (instead of by Chain ID).
• In the Sequence panel
• All the contents of the structure can be identified here - including polymers, non-polymers, waters, ions, and more
• In the Component panel section of the Controls panel
• Select from a variety of preset and default views of different components in the structure. Use these to learn more about the shape and composition of the structure being viewed
• In large complex structures, temporarily hiding one or a few components by clicking on the eye icon next to it may help see different components clearly.

Change representations

• In the Component panel section of the Controls panel
• For an already existing component of interest or a new one being created, click on the “Add Representations” options to change representations to cartoon, ball and stick, spacefill etc..
• Use the Selections options (turned on by clicking on the arrow in the Toggle menu) to
• Select the atom, residue, ligand, polymer chain of interest and create a component with the desired representation.

Examine the neighborhood

To analyze the location, orientation, and interactions of a specific residue or ligand requires (a) selecting it; (b) displaying it along with its neighboring residues/ligands and (c) displaying the covalent and non-covalent interactions in its neighborhood.

• For a specific residue (amino acid/nucleotide) or ligand - Click on the residue/ligand in the 3D canvas or Sequence Panel (while in the Mol* default mode) to zoom in and view the residues and interactions in its neighborhood. Learn more about this options to focus on a residue/ligand.
• For a specific ligand of interest - From the structure summary page of a structure, click on the Ligand Interactions tab in the Small Molecules section of the page to view the ligand and its neighborhood in the structure.
• For a set of residues or ligands - Select the residues/ligands of interest using appropriate Selection logic. To display the residues/ligands in the neighborhood of the selection, activate the selection mode and click on the Add/Union Selections options. From the options available in the pulldown menu that opens up select Manipulate Selections, and then Surrounding Residues (5 ?) of Selections or other options available here. With this selection 2 components should be created - one to display the selected residues/ligands in ball and stick representation and the other to display the Non-covalent interactions in this selection. Learn more about the components logic.

Select all or parts of the molecule to measure, color, label etc.

Viewing, hiding, and changing of representation of one or more components can provide a better understanding of the shape and interactions of the molecule(s) being studied.

Selecting all or parts of the molecule(s) being visualized is the first step in a variety of functions. This will require activation of the Selection Mode of Mol*. Learn more about the Selections Logic.

Using these options you can select an atom, residue or ligand, polymer chain, all instances of a specific entity, etc. Various actions may be applied to the selection and are described here.

Show or Hide

Once the atoms, residues, chains are selected, two options are available - provide specific instructions while the selection is still active or create a component for it to provide instructions later.

• While the selection is displayed with a green halo in the 3D canvas and sequence panel, clicking on the minus sign in the Selection Mode menu to hide it from display on the 3D canvas.
• If a component is created it can be viewed or hidden by clicking on the eye icon next to it in the Components panel. Specific representations of the component can be created to meet the needs of the exploration - e.g., see the molecular surface, cartoon, ball and stick or other representations.

Color

There are three ways to color structures using Mol*.

A. Using Selection Mode

This method is best when seeking to apply a custom color to a structure.

• Select the parts of the structure to be colored in Selection Mode, and while the selection is still active (highlighted in green) click on the (paint brush icon) located in the Selection Mode toolbar to activate the coloring options.
• Choose a desired color using the preset colors or create a new color using the RGB tool or the Lighten/Darken button to select the desired color.
• Click on the Representations options to select the level of selection to which the coloring will be applied.
• Click on the Apply Theme button to color the selection.

Note: This tool can also be used to reset the color of the selection by selecting Reset Color in the Action options.

B. Using the Components Panel

This method is best when seeking to apply a color based on structural properties of a component that has already been created. Click on the button containing three dots in the Components Panel, and then click on the Set Coloring option. There are several submenus which allow the component to be colored according to its structural properties. For example, it can be colored based on chain ID (rainbow from N-terminus to C-terminus), hydrophobicity, secondary structure, etc.

The color schemes listed above use 3 types of palettes - sequential, diverging, and qualitative. Learn more about the color palette options.

C. Using the Quality Assessment panel

Click on the Quality Assessment panel in the controls pane to access ways for coloring the structure based on quality assessment measures for the structure.

Label, Measure

A critical part of 3D structure analysis is to be able to identify and label atoms, residues and polymer chains; and measure distances, angles, and dihedrals. These functions are all enabled from the Measurements panel in the controls panel. Learn more about labeling and measurements.

Customize and Save views

When visualizing, analyzing, and creating figures for publication a few additional aspects of visualization need to be considered. A few such considerations are described here.

Background

To color backgrounds in Mol*, click on the Settings/Controls Information button in the Toggle Menu. Next to the Background option, choose a desired color using the preset colors, or create a new color using the RGB tool or the Lighten/Darken buttons. If the three dots next to the Background option are clicked, an option is provided to make the background transparent.

The color of the background may be changed for specific purposes. To change the background color in Mol*:

• Click on the Settings/Controls Info button in the Toggle Menu.
• Next to the Background option, choose a desired color using the preset colors, or create a new color using the RGB tool or the Lighten/Darken buttons.
• If the three dots next to the Background option are clicked, an option is provided to make the background transparent.

Camera

The camera can view the structure in two different views (Figure 5) - the perspective view (default) shows features that are far away from the camera on a smaller scale compared to those nearby; and the orthographic view where all objects appear at the same scale. While perspective views allow the viewer to assess depth in the object being viewed, orthographic views allow easy comparison of features at scale.

Focus

To zoom in and center on the structural feature being examined use the Focus options. Learn more about Focus options.

Transparency

Sometimes it may be helpful to see through to examine structural features that are behind a specific residue, ligand, or other structural feature. To change the transparency of a representation and surface:

• Select all or part of the structure using options from the Selection Mode.
• Click on the arrow icon in the Toggle menu to view the Selection Mode toolbar.
• Click on the paint brush icon and in the space next to “Action”. From the options displayed, select “Transparency”. Then use the Value slide to set the transparency of the selected structure. A value of 0 is completely opaque, and a value of 1 is completely transparent. Select the desired value of transparency and click on Apply Theme.

A variety of submenus allow customization of molecular surfaces including their transparency. For example, to create a semi-transparent representation of the molecule:

• Select all or part of the structure to display its molecular surface.
• Expand the options for the Molecular surface
• You can change the Opacity settings slider to see through the surface.
• You can also click on the Advanced options >> Shading options >> and Xray shaded mode. In this mode the translucency applies to the molecule such that the rim of surfaces is more opaque so you see the inside of the representation but the silhouette or shape is better emphasized.

Although every representation has these options, it is particularly useful for molecular surface representation. Descriptions of the options will appear in tooltips in the future versions of Mol* library.

Clip Planes

Clipping cuts or slices away parts of structures, surfaces, and objects from view. There are two ways to manually change the clipping planes using Mol*.

• Use Shift + Mouse Wheel to move the front and back clipping planes. On a touchpad, use Shift + two-finger drag.
• Use the settings button and the clipping slider

Note that focusing on an object will automatically change the clipping planes to display the object of interest.

Light and Shade object Ambient Occlusion Effect

In order to appreciate surface details it may be helpful to adjust the light and shading settings.

For example, ambient occlusion is a shading and rendering method used to determine appearance based on how easy light can reach the surface. Areas that are occluded from light (e.g., crevices) are darkened to add realism and perception of volume to the molecule representation. To apply this approach

• Click on the Settings/Controls Info button in the Toggle Menu.
• Next to the Occlusion option, select On.
• Click on the three dots to open additional options and select as appropriate.
• An examples where this function makes an impact is seen in Viruses, e.g., PDB ID 1rb8

Screenshots

Whether it is for record keeping and analysis or for inclusion in publications, posters etc. it is valuable to have easy options to save visual images of the molecule(s) under study. Save images from Mol* as follows:

• Click on the Camera Shutter icon or the Screenshot/State Snapshot button in the Toggle Menu.
• An auto-crop function is available to define the region of the 3D Canvas to include in the screenshot. This is defined by the red/orange box around the molecule(s) in the screenshot preview. The size of this box can be changed as needed.
• You can either Download the image directly to your local directory or copy the image to clipboard. In the latter case the user will be instructed to right click on the image and choose to copy image from the context menu

The State option at the bottom of the Screenshot/State menu allows users to save sessions or state of the molecular visualization. The difference between state and session is as follows:

• State files only contain the description of what to do with the data (e.g., like jmol script, or vmd files)
• Sessions files include data files too (e.g., like pymol files)

Learn more about saving and using state and session files.