Managing the Display

Introduction

The Controls panel is located on the right hand side of the Mol* display and contains options for modification and manipulation of the structure display. Each section of this panel (Structure, Measurements etc.) has several subsections (Figure 1) and is separately discussed here.

Documentation

Structure Panel

The Structure Panel allows the user to view the structure in different forms to meet the needs of the exploration. All structures available from RCSB.org [experimental structures and Computed Structure Models (CSMs)] may be viewed as:

• Model or coordinates of the structure determined - for experimental structures this represents the deposited structure or ensemble, while for CSMs this is coordinates of the predicted structure. Note: the deposited coordinates for experimental structures may or may not represent the structurally stable or biologically relevant assembly of polymer(s) and ligands in the structure.
• Assembly - The assembly coordinates usually represent a form of the structure that has some structural or functional significance. This is the form of the structure loaded to Mol* from the structure summary pages. The assembly coordinates for structures determined using X-ray crystallography or 3DEM may be generated, either by applying specific symmetry operations (crystallographic or non-crystallographic) or by selecting specific subsets of polymers and ligands from the deposited coordinates. NMR structures are commonly deposited as ensembles of structures. The best representative model is made available as the “Assembly” coordinates. The assembly for all CSMs is the same as its corresponding Model (predicted structure).

Note: Even though the assembly form of the structure may not provide any additional understanding about NMR structures and CSMs, they are included to enable structure based query and analysis (e.g., find similar assembly, Structure search, Structure motif search).

Examples: Model and Assembly forms in the Structure panel of a few different structures are included here:

• An experimental structure determined by X-ray crystallography (PDB ID 4hhb) shows options to view the model and various assemblies (Figure 1A). The preset views generated by these options are shown in Figure 2.
• An experimental structure determined by NMR (PDB ID 2n3q) shows options to view the representative model (using the default option), all models in the ensemble, and each model individually by selecting specific one using the slider as in Figure 1B.
• A CSM (from Model Archive MA_MABAKCEPC0002) shows options to view model and assembly both of which are identical to each other (see Figure 1C).
• When more than one structure is loaded into Mol* (e.g., using the standalone version of Mol*), all the structures are listed in the Structure panel (Figure 1D). The Structures menu is useful for selecting a structure to have its components listed in the Components Panel. You can click on the Assembly name for one entry to turn it off so the components of the other are expanded and displayed (Figure 1E). Learn more about toggling on and off structures here.

Figure 2: Examples of Structure Panel options for experimental structures, CSMs, and when multiple structures are loaded into Mol*. Structure panel showing A. an X-ray structure (PDB ID 4hhb) loaded; B. an NMR structure (PDB ID 2n3q) loaded; C. a CSM from Model Archive (MA_MABAKCEPC0002) loaded; D. two structures (PDB IDs 1mbo and 2dn2) loaded.

The Structure panel provides options to select and display the relevant form of the structure for exploration. A sample of different views for the structure in PDB entry 4hhb that can be viewed by clicking on the presets button next to the structure name (see red box marked in Figure 2A) provides a drop-down menu of alternate views of the structure shown in Figure 3 A-D.

Figure 3: Preset views of a crystal structure (PDB entry 4hhb). Explanations of the different forms of the structure shown in sections A-D are included below.

1. Default (Assembly): Creates a structure for assemblies in the file/entry.
2. Unit Cell: Creates a structure that fills the crystallographic unit cell. Only available for X-ray entries.
3. Super Cell: Creates a structure that fills the crystallographic unit cell and all neighbouring unit cells. Only available for X-ray entries.
4. All Models: Creates a structure for each model in the file/entry. Only available for multi-model files/entries.

Under the structure name, you can select the type of view [Model, Assembly, Symmetry Mates, Symmetry (indices), Symmetry (assembly)].

Measurements Panel

The Measurements Panel allows the user to make desired measurements in a structure ( add labels, measure distances, measure angles, measure dihedral angles)

To make measurements, use the following steps:

• Click on the Add button and a drop-down menu will show up.
• Activate the Selection mode and select the appropriate number of atoms in the 3D canvas. Without the appropriate number of selections, the measurement options will not be available for use. Select
• one atom to label it,
• two atoms to measure distance,
• three atoms to measure angles, and
• four atoms to measure dihedral angles.
• Select and click on the desired measurement operations (Figure 4).

Within the Measurements Panel, the selections can be toggled up and down using arrows that show up next to them. This allows the user to make all of their selections first and then specifying which of the selections should be used for the measurements (toggling them up to the top of the selections listing). Additionally, the options button next to the Add button gives the option to change the units in which distance is measured, as well as color options for the text display on the 3D canvas.

Note: The measurement will be made based on which Picking Level is used for the selections. When the selections are atoms, the measurements will be made from the center of the atoms. If another Picking Level, such as residues or chains, is used, the measurements will be made using points from the center of the space that the selection occupies. This means that if three residues are selected for an angle measurement, the angle will not be taken from the alpha carbon, but from a point from the center of the space the residue takes up.

Add Labels

In order to label a part of the structure, one selection needs to be made. In this example, one atom from the structure 4HHB was selected. Once this is done, the Labels option is available. Click on it and a label will show up on the 3D canvas, as well as a new Labels menu under the Controls (Figure 5).

In the Labels menu:

• You can choose to hide the label on the 3D canvas by clicking on the eye icon, and clicking on it again will show the label
• You can delete the label by clicking on the trash icon.
• You can click on the rightmost icon (three dots) to reveal a drop-down menu with Options and Advanced Options, which can be used to adjust the display of the label on the 3D canvas.

Measure Distances

In order to measure distance, two selections must be made. In this example, two atoms from the structure 4HHB were selected. Once this is done, click on the Add button under the Measurements Panel. Under this, the measurement options will be shown, as well as any selections made. The Distance option is now available. Click on it and the distance will be measured and displayed both in the 3D canvas, as well as under a new Distance menu under the controls (Figure 6).

The icons in the Distances menu perform the same functions as those in the Labels menu. See Add labels for more information.

Measure Angles

In order to make angle measurements, three selections need to be made. In this example, three atoms from the structure 4HHB were selected. The order in which the selections are made will affect the angle that is measured. The second selection will be the vertex of the angle, so make selections accordingly. Once three selections are made, the Angle option is available. Click on it, and an angle measurement will show up on the 3D canvas, as well as a new Angles menu under the Controls (Figure 7).

The icons in the Angles menu perform the same functions as those in the Labels menu. See Add labels for more information.

Measure Dihedral angles

In order to make a dihedral angle measurement, four selections need to be made. In this example, four atoms from the structure 4HHB were selected. The order in which the atoms are selected will affect the angle that is measured. The second and third selections represent the line along which the angle between the first and fourth selections is measured. Once the selections are made, the Dihedral option will be available. Click on the Dihedral option, and a dihedral angle measurement will show up on the 3D canvas, as well as a Dihedrals menu under Controls (Figure 8).

The icons in the Dihedrals menu perform the same functions as those in the Labels menu. See Add labels for more information.

Structure Motif Search Panel

This section provides options to select residues in a structure to launch a structure motif search. This type of search may be applied to both experimental structures and CSMs. Learn more about Defining queries using Mol*.

Components Panel

Components are representations of certain parts of the structure being visualized. For more information, see Components Logic. The Components Panel shows options for the manipulation and display of the contents of the structure(s) being viewed. Various options are available for components to be added to the components panel:

Presets

By default, when a molecule is loaded into Mol*, it is displayed as Polymer & Ligand, where polymers are shown in the cartoon representation, while ligands and waters are shown in the ball and stick representation. Additional components can be added by selecting groups of atoms, residues, or chains.

Clicking on the Preset button presents options for changing the representation and components shown (Figure 9).

An example of various components and their representations available from this menu for a specific structure are shown in Figure 10.

Figure 10: Preset views available for PDB entry 2dn2. The section labels A, B, C1-5, D, E1-4 are described below.

1. Empty: Removes all representations to give you a blank slate to work with.
2. Automatic: Chooses a Basic preset based on the size (residue count, number of symmetric chains) of a structure. Smaller structures are shown with more detail than larger ones, ranging from atomistic display to coarse surfaces.
3. Basic: Various preset display options include
1. Atomic Detail: Shows everything in atomic detail with Ball & Stick representation.
2. Polymer Cartoon: Shows polymers in Cartoon representation.
3. Polymer & Ligand: Shows polymers as Cartoon, ligands as Ball & Stick, carbohydrates as 3D-SNFG (Symbol Nomenclature For Glycans) and water molecules semi-transparent.
4. Protein & Nucleic: Shows proteins as Cartoon and RNA/DNA as Gaussian Surface.
5. Coarse Surface: Shows polymers as coarse Gaussian Surface.
4. Miscellaneous: The Illustrative view shows the molecule as a stylized spacefill representation where the carbon atoms in the polymers and ligands have a lighter hue compared to the heavier nitrogen and oxygen atoms. This representation was inspired by the style used in the Molecule of the Month features.
5. Annotation: These features are colored based on specific analysis of the structure.
1. Assembly Symmetry: Same as ‘Automatic’ preset but colored by Assembly Symmetry Cluster membership and showing Assembly Symmetry axes and polyhedron cage.
2. Validation Report (Geometry Quality): Same as ‘Automatic’ preset but colored by Geometry Quality and displaying geometry clashes as pink disks.
3. Validation Report (Density Fit): Same as ‘Automatic’ preset but colored by Density Fit. Only shown/available for X-ray entries.
4. Validation Report (Random Coil Index): Same as Automatic preset but colored by Random Coil Index. Only shown/available for NMR entries.

What is shown?

Components that can be viewed in the panel (Figure 11) include:

• Default list of components (Figure 11A)
• Polymers (including proteins and nucleic acids)
• Ligands (small molecules such as inhibitors, cofactors)
• Waters
• Ions (such as Na, Zn, SO4)
• Carbohydrates (saccharides such as glucose, galactose)
• A visual representation of the unit cell is available (for structures solved by X-ray crystallography), and can be enabled by clicking the eye icon next to the Unit Cell option.
• Additional Components (Figure 11B)
• Selection is made while in default mode, then the focused region will include two components: [Focus] Target, [Focus] Surroundings (5 Å).
• Added components created by the used (including a selected set of atoms, residues, polymers)

Figure 11: Components panel - A. List of components showing options for changing their representation, coloring, and modifying selections of a component (e.g., for Polymer); B. Examples of additional components added by clicking on any part of the structure to focus on it and examine its neighborhood, and New Components that can be added by selecting specific residues, polymers etc.

Additional components can be created in the following two ways:

1. Clicking on any part of the structure (to make a selection) while in default mode of Mol*. This action focuses on the selection “[Focus] Target” and displays the residues, ions, waters, and ligands in the 5 Å neighborhood “[Focus] Surroundings (5 Å)” along with interactions between these atoms and residues (Figure 12)

2. A component can be added by making a selection and either using the Components icon in the Selection Mode toolbar or using the Add button in the Components Panel under Controls (Figure 13).

How are components shown?

For all components listed in the components panel, the icons next to each component perform similar functions as seen in the Measurements Panel.

When the options icon (three dots at the far right end of the row) is selected (see Figure 11A), various options are available to:

• Add Representation: Can choose the representation of that component (cartoon, ball-and-stick, Gaussian, etc.)
• Set Coloring: Choose the coloring of the component
• Modify by Selection: Gives selection options given in the Selection Mode toolbar

Each of these functions are described in further detail here.

The following representation options are available for the components:

Add Representations

By default the polymers (proteins and nucleic acids) are represented as cartoons, while ligands, ions, and waters are represented as Ball & Stick. For large structures (like icosahedral viruses) the polymer chains may be represented using the Gaussian surface. Structures with carbohydrates are displayed using two representations - Ball & Stick and Carbohydrate representations. The default representations may be hidden and or removed from the display by clicking on the eye and trash can icons, respectively. Many additional representation options are available for the components. An example of various representations available from this menu for a specific structure are shown in Figure 14.

Figure 14: Representations of molecules available from Mol* for PDB ID 4hhb (panel A-N), and PDB ID 5elb (panel O). Descriptions of each of these representations are included below.

1. Cartoon: This shows that backbone atoms of the polymers (Cɑ atoms in proteins and Phosphorus atoms of the Phosphate groups in nucleic acids), and connects them with a ribbon drawing. This is also referred to as the ribbon representation. Since only the representation of the polymer was changed, ligands present in the structure are shown in Ball & Stick representation. This is true in most of the representations discussed here.
2. Backbone: This shows the Cɑ atoms in the protein structure and links them with a stick in the order that they appear in the polymer (i.e., Cɑ1 is linked to Cɑ2, which is linked to Cɑ3 and so on).
3. Ball & Stick: This representation shows all atoms in the structure as small balls and covalently bonded atoms are connected by a stick.
4. Gaussian Surface: This representation draws a closed surface on all atoms of similar density for a polymer (protein or nucleic acid). Each atom in the polymers is represented by a sphere, where the spheres of covalently bound atoms touch each other to create a continuous surface. Note that changing the Size Theme option to Physical displays the surface at approximately the Van der Waals radii and shows the overall shape and size of the polymers.
5. Gaussian Volume: This representation shows the spatial distribution of electron density within the molecule, and can provide insights into the chemical bonding within the molecule.
6. Label: This representation displays the amino acid type (Ala, Lys, Tyr, etc.,) and their sequence order in the polymer.
7. Line: This representation is similar to the Ball & Stick representation, only the atoms are represented as points (instead of balls) and the covalent linkages are shown as lines.
8. Molecular surface: This shows the solvent exposed surface of the molecule. It is computed by rolling a sphere (usually with a radius of 1.4 Å to approximate a water molecule), around the van der Waals surface of the molecule. This representation is useful for visualizing cavities and pockets on the surface of the molecules where small molecules, drugs, inhibitors may bind or to explore protein-protein interfaces. Note the molecular surface may be colored by hydrophobicity (or in other visualization tools by charge) to estimate the nature of interactions in these pockets and cavities.
9. Orientation: This representation shows the overall shape of each polymer as an oval, with their principal axes passing through the center of mass. It provides a rough estimate of where the polymer is positioned in the structure. Atomic details are not visible in this representation.
10. Point: This representation shows each polymer building block (amino acids and nucleotides) as points in space.
11. Putty: This representation is a stylized cartoon representation where the backbone of the polymers are shown as a thin flexible tube or noodle like structure.
12. Spacefill: This representation shows each atom in the polymers as a sphere with its Van der Waals radii and provides a sense of the volume occupied by the atoms of the polymer. This is also known as the CPK (Corey-Pauling-Koltun) mode.
13. Non-covalent interactions: This representation shows the common non-covalent interactions present in the polymers (mostly H- bonds), as dashed lines.
14. Validation Clashes: This representation shows clashes between atoms within a structure indicating poorly modeled regions of the structure. Hovering over any of the discs that are displayed show the extent of the clash and the identity of the atoms involved in the clash.
15. Carbohydrate: This representation is limited to carbohydrate containing structures, where the saccharide monomers are displayed using the SNFG representation. Learn more about the SNFG representation.

This same set of representation option are also available by clicking on the cube icon, when using the Selections options (turned on by clicking on the arrow in the Toggle menu, Figure 15)

Set Coloring

By default the polymers are represented as cartoons and colored by chain ID, while ligands, ions, and waters are shown in the Ball & Stick representation and colored according to the CPK color scheme (i.e., red for oxygen, blue for nitrogen, etc.), except the carbon atoms’ color matches the chain identifier. Chain IDs are assigned to ligands based on their proximity to or association with a polymer chain. Carbohydrates are usually represented both in the SNFG and Ball & Stick representations and colored according to the SNFG coloring scheme. The various coloring options available for marking and communicating specific types of information about the structure are described here and shown in the context of a specific PDB entry.

A. Atom Property
Various properties of key atoms in the structure (e.g., atom/element type, order in the polymer chain, occupancy, disorder) can be showcased using colors.
Note: The cartoon representation is used in the examples shown here (i.e., only the backbone carbon atoms are shown). Options available to color by specific atom properties include coloring by:

a. Atom ID: This color scheme assigns discrete and specific colors to each type of atom in the structure. Since the cartoon representation of a protein displays only its CA or C-alpha atoms, the protein polymer chains are colored by the CA atom color (Figure 16). These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3 and 4) and selecting from the various Qualitative color palettes available. Learn more about color palettes.

b. Element Index: This color scheme assigns a range of diverging colors to the atoms in the structure from its beginning (red) to end (blue). Note that the color scheme spans all polymer chains present in this structure. The default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) in Figure 17.

c. Element Symbol: This color scheme assigns discrete and specific colors to each element type in the structure. Since the cartoon representation of a protein displays only its CA or C-alpha atoms, the protein polymer chains are colored by the carbon element color. However, to denote that there are two polymer chains in this structure, the carbon atoms in this representation are colored by chain ID, as can be seen by clicking on the three dots at the end of the Color Theme row in the control panel to view the various options available (Figure 18). These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) and changing the Default setting to Custom.

d. Occupancy: This sequential color scheme assigns amino acid residues in the structure a range of colors according to their occupancies from zero, where the atom is not present, (colored white) to one, where the atom is present and always in that location, (colored purple). The color scheme is shown in Figure 19. These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) and selecting from custom sequential color palettes. Learn more about color palettes.

e. Uncertainty/Disorder: This diverging color scheme assigns amino acid residues in the structure a range of colors according to the uncertainty or disorder, as indicated by its B-factor or root mean square fluctuation (RMSF). The range spans from zero (low B-factor, colored blue) to 100 (high B-factor, colored red). The color options are shown in Figure 20. This coloring option depends on data availability and the experimental method used for structure determination. These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) and selecting from custom diverging color palettes. Learn more about color palettes.

B. Chain Property
Various properties of the polymer chains present in the structure (e.g., chain identifiers, sequence, source of polymer, number of copies ) can be showcased using colors. Options available to color by polymer chain properties include coloring by:

a. Chain ID: This is the default color scheme where each polymer chain is colored in a different color according to its chain identifier (Chain ID) or asym_id in the PDBx/mmCIF format file (Figure 21). These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) and selecting from custom diverging color palettes. Learn more about color palettes.

b. Chain Instance: In this qualitative color scheme, each instance of a polymer chain is colored in a different color using the qualitative color scheme. Therefore the two copies of the polymer chain shown here are colored in slightly different shades of green as shown in the color key (Figure 22).

c. Entity ID: In this qualitative color scheme, each type of component (polymers like proteins and nucleic acids or small molecules like ions, inhibitors, and drugs) is colored in a different color. In the structure colored in this color scheme (Figure 23), there are two copies of the polymer chain, so both the protein chains are shown in the same green color.

d. Entity Source: In this qualitative color scheme, the polymers are colored by the source from which they are derived. Figure 24 shows an example of a chimeric protein - one part of which is an E. coli protein (colored green) and another part is derived from yeast (colored orange). There are two copies of the polymer chain, so both copies of the protein chain follow the same color scheme.

e. Model Index: In this color scheme, the polymers are colored by the Model index. Figure 25 shows an example that has only one model (with model index 1) so the protein is colored in a single color (green).

f. Polymer Chain ID: This is similar to the default color scheme (color by Chain ID) where each polymer is colored by its Chain ID or asym_id value. Figure 26 shows an example where there are two polymer chains colored in two different colors.

g. Polymer Chain Instance: This color scheme is similar to the color by Chain Instance color scheme, specifically applied to polymer chains. Figure 27 shows an example where there are two copies (or instances) of the polymer chain, so they are colored in two different colors.

h. Structure Index: In this color scheme the entire structure is assigned a single color. When multiple structures are simultaneously uploaded to the same session of Mol*, each structure is assigned a different index. Figure 28 shows an example where there is a single structure, so all polymer chains of the structure are colored green.

C. Miscellaneous
In addition to atom, residue, and polymer chain properties, a variety of other properties (e.g., polymer type to non-covalent interaction type) can be showcased using colors. Options available to color by miscellaneous properties include coloring by:

a. Cartoon: In this color scheme, when the structure is shown in the cartoon representation, each entity type (e.g., proteins, DNA, RNA, ions, waters) is colored in a different color. If the building blocks, such as amino acids and nucleotides are shown, then each residue is colored in its specified color. Figure 29 shows an example where there are two copies of a protein (colored light purple).

b. External Volume: In this color scheme the structure is colored by a default color - gray in the example below (Figure 30). This can be changed to another color of choice by clicking three dots in the far right of the row “Color Theme” to view the color options and then clicking on the gray colored box next to “Default Color” and selecting a different color from the options presented.

c. Illustrative: This color scheme is similar to the Cartoon color scheme described above, where each entity type (e.g., protein, DNA, RNA, ion, water) is colored in a different color. Figure 31 shows an example where there are two copies of a protein (colored light purple).

d. Interaction Type: This color scheme applies to the non-covalent interactions shown. Figure 32 shows a variety of different interactions between the atoms and residue displayed, e.g., hydrogen bonds, ionic bonds, pi-stacking etc.

e. Uniform: In this color scheme the polymers are colored using a uniform color. The default color used is shown in Figure 33. This can be changed to another color of choice by clicking three dots in the far right of the row “Color Theme” to view the color options and then clicking on the gray colored box next to “Value” and selecting a different color from the options presented.

D. Residue Property

Various properties of the polymer building blocks (also called amino acids or residues) present in the structure (hydrophobicity, exposure to solvent, residue type, secondary structure, order in a polymer chain etc.) can be showcased using colors. Options available to color by residue properties include coloring by:

a. Accessible Surface Area: In this color scheme the backbone atoms of the polymer are colored by its side chain’s solvent accessible area. Buried amino acids are colored blue/green, while exposed amino acids are colored orange/red (Figure 34). Displaying the amino acids using the Molecular Surface representation can produce a more impactful view of the surface exposed and buried amino acids, as well as pockets and cavities in the structure.

b. Carbohydrate Symbol: This color scheme applies specifically to carbohydrates (small molecule components and polymers) present in the structure as specified by SNFG (Figure 35). Learn more about the SNFG format.

c. Hydrophobicity: In this color scheme the backbone atoms of the polymer are colored by the hydrophobicity of its side chain. Hydrophobic amino acids are colored green, while hydrophilic amino acids are colored orange/red (Figure 36).

When a Molecular Surface representation is shown, coloring the surface by this color scheme can help identify hydrophobic and hydrophilic patches/pockets in the structure.

d. Molecule Type: This color scheme is similar to the Cartoon and Illustrative color schemes, described above. The backbone atoms of the polymers and small molecular components (e.g., protein, DNA, RNA, ion, water) are each colored in a different color. Figure 37 shows an example where there are two copies of a protein (colored light purple).

e. Residue Name: In this color scheme the backbone atoms of the polymer are colored by the type of amino acid side chain as specified in the key (Figure 38).

f. Secondary Structure: In this color scheme the backbone atoms of the polymer are colored by the secondary structural conformation that it adopts. By default the alpha helices are colored in a bright pink color, beta strands are colored a golden yellow etc. (as shown in Figure 39). These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3) and changing the Default setting to Custom.

g. Sequence ID: In this color scheme the backbone atoms of the polymer are colored by the order in which it appears in the polymer sequence - Where the beginning (in a protein N-terminal) residues are colored blue/violet and the ending (in a protein C-terminal) residues are colored red. The residues in between are colored according to the colors of the rainbow (Figure 40). Sometimes this coloring scheme is also called the rainbow or spectral colors. These default colors can be changed by clicking on the Color Theme’s additional options (labeled 3).

E. Symmetry

PDB structures (especially ones determined using macromolecular crystallography) may include various assemblies, some of which may be biologically relevant, while others may be formed due to specific crystal packing. Options available to color by possible assemblies of the structure include coloring by:

a. Assembly Symmetry Cluster: In this color scheme each assembly in the structure (either defined by the author or computed using specific software) is colored in a specific color (Figure 41).

b. Operator HKL: This color scheme can be appreciated when symmetry related molecules are displayed. Generate these symmetry related molecules by clicking on the Symmetry Mates option in the Structure panel. Figure 42 displays several symmetry related copies of the structure in PDB ID 4rg5. The copies are colored by the symmetry operations used to generate them. Here 555 represents identity or no translation in x, y, and z directions of the assembly being viewed. Symmetry related molecules generated by translating molecules along the negative x axis would be represented as 455. Specific colors assigned to these hkl symmetry molecules can be viewed by clicking on the Color Theme key (arrow labeled 2 in Figure 42).

c. Operator Name: In this color scheme the symmetry related molecules are colored by combinations of their specific symmetry operators in the space group (represented by the number before the underscore) and their translations along the x, y, and z axes (represented by the three numbers listed after the underscore). In Figure 43, these operator names are listed as 1_555 represents identity, while 2_555 represents symmetry equivalent 2 in the same unit cell, etc.

F. Validation

Various quality measures are used to assess the accuracy of biomolecular structures. These measures include fit to electron density (for crystal structures), random coil index (for NMR structures), map-model fit for EM structures, and pLDDT scores (for computed structure models) may be mapped on the structure to visualize structure quality. Learn more about structure quality measures.

Options available to color structures by structure quality include coloring by:

a. Density Fit: This option applies mostly to structures determined by macromolecular crystallography. It uses a diverging color scheme to represent a poor (red) to better (blue) fit of the structure to the electron density (Figure 44). Clicking on any of the residues in this representation displays the Real Space R Z-score value for it. Learn more about RSRZ scores.

b. Experimental Support Confidence: This color scheme uses discrete colors to represent residues that range from very well resolved to very low confidence (Figure 45). The confidence level is measured by the real space correlation coefficient (RSCC). Learn more about RSCC.

c. Geometry Quality: This color scheme displays residues in a polymer with geometry issues (such as clashes and outliers) in the structure. Clicking on the additional options (three dots) at the end of the Color Theme row opens additional options to select which types of geometric issues to be reported (Figure 46).

Modify Selection

To modify a selection within a component, first make a selection, and choose Modify by Selection for the component of choice within the Components Panel, and choose one of these options:

• Include - This will include the selection in the component
• Subtract - This will remove the selection from the component
• Intersect - This will change the component to be the intersection between the original component and the selection

Additionally, the Options button next to the Add button under the components panel allows for adjustments for the representation of non-covalent interactions (Figure 47). Display of hydrogen atoms in the visual can be toggled on and off. Additionally, clicking Non-covalent interactions yields a drop down menu with various types of non-covalent interactions. These can be toggled on and off for display in the non-covalent interactions representation. Additionally, clicking on the options button (three dots) next to any of the interactions yields a drop down menu for various parameters for that interaction. This menu can be used to tweak the parameters for calculation for any of the interactions.

Density Panel

The Density Panel gives options to display the electron density maps used to determine the structure in the 3D canvas. This option is only available for structures solved by X-ray crystallography or cryogenic electron microscopy. When enabled, the display of each of the maps can be adjusted using the sliding bars available (Figure 48).

Visualization of the maps can be adjusted by clicking the + icon next to each map, which will give a drop-down menu of options. They can be shown by a wireframe, which can be turned on by clicking next to the Wireframe option. The color of each map can be changed in this map, as well as the opacity of the map.

View of the maps can be adjusted by clicking on the drop-down menu next to the View button, which gives options to view the maps in different settings. In this menu, the density maps can be turned off, as well as adjusted to be shown around a focus, for the whole structure, or for a bounded box. For the bounded box, the user can select the coordinates of the bottom left and top right corners of the box within which the density maps will be displayed.

In order to view any changes made within this panel, click Update at the bottom of the panel.

Quality Assessment Panel

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Videos: Quality of Computed Structure Model and Visualizing Structure Quality

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This panel provides options to color the structure with polymer building block or residue (e.g., amino acid, nucleotide) level quality indicators. Visualizing parts of the structure that have geometry violations, disagreement with experimental data, or limited/missing data can warn PDB data users that any structural and functional details or evolutionary implications about these parts should be considered with caution.

At present, the following types of quality measures (see Figure 49) are available:

• Experimentally determined structures may be colored based on:
• Validation Report
• Based on the wwPDB validation report, this coloring scheme indicates the number of geometry related problems for a specific residue (e.g., geometry outliers, and clashes) as follows:
• Blue = 0 problems
• Yellow = 1 problem
• Orange = 2 problems
• Red = 3 or more problems.
• Mousing over any residue in the structure displays the specific type of problems identified for that residue in the bottom-right corner of the 3D-Canvas. Details about electron density fit for the specific residue are also listed here. Learn more about the RCSB PDB Validation report coloring scheme.
• Experimental Support Confidence
• To assess how well the atomic coordinates for an individual residue are supported by the X-ray crystallographic experimental data, a quality assessment measure was developed, based on individual residue Real Space Correlation Coefficient (RSCC) values (Shao et al., 2022).
• Individual RSCC values vary with both residue chemical structure and structure resolution. Therefore, the RSCC values for each type of amino acid (e.g., Gly, Ala, Val), present in a very large number of PDB structures determined by X-ray Crystallography, and in different resolutions bins (e.g., 1-1.1 Å, 1.1-1.2 Å) were ranked from lowest to highest, indicating worse to better experimental data support for residue atomic coordinates.
• Amino acid residues in any PDB structure can be colored by their RSCC value ordinal ranking as follows:
• Blue = 25% - 100% - very well resolved residues, very high confidence
• Cyan = 5% - 25% - well resolved residues, high confidence
• Yellow = 1% - 5% - outlier residues,low confidence
• Orange = <1% -, extreme outlier residues, very low confidence

Only the 20 standard amino acids and seleno methionine within a polymer entity that have computed RSCC values are colored by this quality assessment measure. The complete RSCC value distribution lookup table for each amino acid type, by resolution is available here.

Note the following exceptions:
1. Structures determined by experimental methods other than X-ray crystallography (e.g., NMR, and EM) do not have options for coloring by Experimental Support Confidence. See example.
2. Structures determined using X-ray crystallography for which RSCC are not available (i.e., cannot be calculated because structure factor data are not available) display an error message “Failed to obtain RSCC values”. See example.
3. Non-standard amino acids (e.g., phosphotyrosine), nucleic acids, carbohydrates, ligands, and water molecules are all marked gray. See example.

• Computed structure models (CSMs) loaded into Mol* may be colored based on:
• pLDDT (predicted local distance difference test) confidence score (see Figure 50)
• This coloring scheme is based on an individual amino acid residue-level confidence score developed by DeepMind for the AlphaFold2 project (Jumper et al., 2021). It ranges between 0 and 100, and is described in detail in Tunyasuvanakool et al., 2021. According to this color scheme
• Blue = Very high confidence (> 90)
• Cyan = Confident (between 90 and 70)
• Yellow = Low confidence (between 70 and 50)
• Orange = Very low confidence (< 50)

Note: Regions of a CSM with pLDDT scores below 50 are likely be disordered (Ruff and Pappu, 2021), assuming the protein is not interacting with another macromolecule and/or a ligand(s).

Assembly Symmetry Panel

The Assembly Symmetry Panel demonstrates any symmetries within the molecule when displayed in Assembly mode. Once enabled, any symmetries that are in the molecule will be available as a drop-down menu to display and visualize on the 3D canvas (Figure 51). Additionally, the coloring of the symmetry can be adjusted.

Export Models

The Export Models panel (Figure 52) allows users to download the 3D structural data loaded into the viewer as .CIF files. The export panel is made available when at least 1 structure is loaded. The structure files can be saved locally in the default download location in either mmCIF or Binary mmCIF format (Sehnal et al., 2020).

Export Animation

The Export Animation panel (Figure 53) allows users to easily create and export molecular animations as videos.

• The available options include:
• Animate Trajectory: can be used to animate multiple models (e.g., NMR data: /3d-view/1nmr). The animation renders one model after another and combines them into a .mp4 video.
• Camera Spin: gives a molecule 360 spin around the vertical axis. The rotation can be performed clockwise or counterclockwise.
• Unwind Assembly: animates a process of transforming chain copies from an asymmetric unit to an assembly by sequentially applying transformations to all chains.
• Control the output file size select the following video output options:
• Click on the screenshot icon in the Toggle menu
• Expand the viewport options to select a lower resolution to yield a smaller file size.

• Control the position of the molecular rotation axis ((Figure 54) as follows:
• The default rotation axis is along the vertical axis.
• Change the orientation of the molecule to see a desired view.
• Using camera orientation axes (triangular element located in the left lower corner) can help quickly reorient the molecule.

Export Geometry

This panel allows users to save 3D objects in the binary .glb format. These files can be used to save 3D scenes, models, lighting, materials, node hierarchy and animations for transfer to other tools and platforms.

Import Panel

(Only available at rcsb.org/3D-view)

The Import Panel (Figure 55) enables users to upload multiple molecular structures into Mol* to compare them or perform superpositions. The Import Panel can only be accessed at rcsb.org/3D-view and is located at the top of the Controls Panel.

There are two ways to import files into Mol*:

Open Files: The Open Files menu is used to upload structures from computer files. The acceptable formats for these files may be seen by clicking on the words Volume, Coordinates, Trajectory etc.(Figure 55 B). The menu also provides structure display options. To automatically view the structure in the 3D canvas, set Visuals to “On.” After a file is selected and the desired options are chosen, click “Apply” to upload the structure.

Download Structure: The Download Structure menu is used to access or download structures directly from various archives such as the PDB, PDB-Dev, SWISS-MODEL, AlphaFold DB, Model Archive, or PubChem by inputting IDs/accession codes (Figure 55 B). The identifiers of multiple structures can be listed at once by separating them with commas (Figure 55 C). After the identifiers have been inputted, click “Apply” to upload the structures.

Session Panel

(Only available at rcsb.org/3D-view)

The Session Panel enables users to save sessions and views. Sessions are downloaded as computer files which can be opened in Mol* at any time. In addition, users can share session files with others to collaborate. Within a Mol* session, users are able to create “views” which contain all the information in the 3D canvas at the time the views were saved. Multiple views can be saved in a single session. The Session Panel can only be accessed at rcsb.org/3D-view and is located in the Controls Panel.

• Saving Views: The Views menu is used to save views in Mol*. Users can name views and write a description for each one. After clicking “+ Add,” the view will be saved in the Views menu for the entirety of the session (Figure 56 A).
• Deleting/Replacing Views: The Views menu contains a list of all saved views. Next to each view is a trash can icon (Figure 56 B). Clicking that icon allows the view to be deleted from the Mol* session. To replace a view, click on the horizontal parallel arrows icon. This will replace the view with the current view in the 3D canvas. Deleting and replacing views are actions that cannot be undone.
• Opening Saved Views: There are two ways to open saved views in Mol*.
• All saved views will be listed in the Views menu (Figure 56 C). Click on a view to open it.
• If multiple views are saved, they can be accessed using a drop-down menu at the top of the 3D canvas. Clicking on a view will open it. The order in which the views are listed depends on the time they were saved. To reorder the views, use the up and down arrows next to each view in the Views menu. In default mode, use the arrows pointing left and right to switch between saved views.
• Cycle Through Saved Views: In default mode, click the “play” button in the toolbar at the top of the 3D canvas to cycle between all saved views. Click the “stop” button to stop cycling between them.
• Download/Open Menu: The Download/Open menu allows users to save sessions and states. It also allows them to be reopened at any time.

Figure 56: Options to A. create, B. delete and C. view sessions.

Superposition Panel

(Only available at rcsb.org/3D-view)

The Superposition Panel rotates and translates molecular structures to make them match other structures. Mol* performs superpositions by matching selected chains or atoms. The root-mean-square deviation (RMSD) of the superposed structures will be listed in the Log Panel at the bottom of the application window. To access the Superposition Panel, two or more structures must be uploaded at rcsb.org/3D-view. The Superposition Panel will appear in the Controls Panel next to the 3D canvas.

To access the Superposition Panel, two or more structures must be imported at rcsb.org/3D-view. These may be experimental structures or CSMs, that are uploaded from saved files or downloaded (called) from various public data resources. The Superposition Panel (Figure 57) will appear in the Controls Panel next to the 3D canvas.

Superposing by Chains: In order to superpose structures by chains (Figure 58), two or more selections from separate structures are required. Regions of a chain can also be selected for superposition. For each PDB entry, selections must be limited to single polymer chains per structure. If using a region of a chain, only one region per chain can be used for each structure. After making two or more selections, click “Superpose” to superpose the structures in the 3D canvas. While the superposition is per chain, the resulting 3D transformation is always applied to the whole structure. When superposing more than two structures, note that the alignment is done to the first structure. The RMSD will be listed in the Log Panel.

Superposing by Atoms: In order to superpose structures by atoms (Figure 59), one or more atoms from separate structures must be selected. Select one or more atoms and click “Superpose” to superpose the structures in the 3D canvas. The superposition is done on all given pairs of atoms in the order they appear in the panel. To reorder the atoms, use the up and down arrows in the panel. The RMSD will be listed in the Log Panel.

Note: Explore the Pairwise Structure Alignment tool for another option for superposing 3D structures.

References:

• Jumper, J., Evans, R., Pritzel, A. et al. (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2
• Ruff, K.M. and Pappu, R.V. (2021), AlphaFold and Implications for Intrinsically Disordered Proteins, Journal of Molecular Biology, 433, 167208, https://doi.org/10.1016/j.jmb.2021.167208.
• Sehnal D, Bittrich S, Velankar S, Koča J, Svobodová R, et al. (2020) BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management. PLOS Computational Biology 16(10): e1008247. https://doi.org/10.1371/journal.pcbi.1008247
• Shao, C., Bittrich, S., Wang, S., and Burley, S.K., (2022) “Assessing PDB Macromolecular Crystal Structure Confidence at the Individual Amino Acid Residue Level”, Structure, 30(10):1385-1394.e3. https://doi.org/10.1016/j.str.2022.08.004.
• Tunyasuvunakool, K., Adler, J., Wu, Z. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596 (2021). https://doi.org/10.1038/s41586-021-03828-1