Managing the Display
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.
|Figure 1: Options in the Controls Panel - red box mark the options seen in all RCSB Mol*, while the ones outside the box are only seen in the stand-alone version of Mol* (rcsb.org/3D-view)|
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.
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.|
- Default (Assembly): Creates a structure for assemblies in the file/entry.
- Unit Cell: Creates a structure that fills the crystallographic unit cell. Only available for X-ray entries.
- Super Cell: Creates a structure that fills the crystallographic unit cell and all neighbouring unit cells. Only available for X-ray entries.
- 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)].
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).
|Figure 4: Measurement panel options - A. Click on the + Add to view options (shown in B.); Click on the options icon next to the + Add button to specify text color etc.|
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.
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.
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.
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*.
The Components Panel shows options for the manipulation and display of the contents of the structure(s) being viewed. Components are representations of certain parts of the structure being visualized. For more information, see Components Logic.
By default, the preset that shows up when a structure is Polymer & Ligand, in which the polymers, ligands and water components are shown. Additional components can be added by selecting groups of atoms, residues, or chains.
The components shown and their representations depend on the structure, what preset is chosen, and what components are created. See an example of various components and their representations in a specific structure (Figure 9).
|Figure 9: Preset views available for PDB entry 2dn2. The section labels A, B, C1-5, D, E1-4 are described below.|
- Empty: Removes all representations to give you a blank slate to work with.
- 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.
- Basic: Various preset display options include
- Atomic Detail: Shows everything in atomic detail with Ball & Stick representation.
- Polymer Cartoon: Shows polymers in Cartoon representation.
- Polymer & Ligand: Shows polymers as Cartoon, ligands as Ball & Stick, carbohydrates as 3D-SNFG (Symbol Nomenclature For Glycans) and water molecules semi-transparent.
- Protein & Nucleic: Shows proteins as Cartoon and RNA/DNA as Gaussian Surface.
- Coarse Surface: Shows polymers as coarse Gaussian Surface.
- 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.
- Annotation: These features are colored based on specific analysis of the structure.
- Assembly Symmetry: Same as ‘Automatic’ preset but colored by Assembly Symmetry Cluster membership and showing Assembly Symmetry axes and polyhedron cage.
- Validation Report (Geometry Quality): Same as ‘Automatic’ preset but colored by Geometry Quality and displaying geometry clashes as pink disks.
- Validation Report (Density Fit): Same as ‘Automatic’ preset but colored by Density Fit. Only shown/available for X-ray entries.
- Validation Report (Random Coil Index): Same as Automatic preset but colored by Random Coil Index. Only shown/available for NMR entries.
Components that can be viewed in the panel by default are
- Polymers (including proteins and nucleic acids)
- Ions (such as Na, Zn, SO4)
- Ligands (small molecules such as inhibitors, cofactors)
- Carbohydrates (saccharides such as glucose, galactose)
- Added components created by the used (including a selected set of atoms, residues, polymers)
- Additionally, if a selection is made while in default mode, then the focused region will include two targets as well: [Focus] Target, [Focus] Surroundings (5 Å).
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 10).
The icons next to each component perform similar functions as seen in the Measurements Panel.
When the options icon for a component is selected, various options are available (Figure 11).
- 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
A visual representation of the unit cell is also available, and can be enabled by clicking the eye icon next to the Unit Cell option.
|Figure 11: Options for changing representation, coloring, and modifying selections of a component (e.g., Polymer)|
The following representation options are available for the components:
- Ball & Stick
- Gaussian Surface
- Gaussian Volume
- Molecular surface
- Non-covalent interactions
- Validation Clashes
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 12). 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.
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 13).
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
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 14) 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 15)
- 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 16). Additionally, the coloring of the symmetry can be adjusted.
The Export Models panel (Figure 17) 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).
The Export Animation panel (Figure 18) 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 19) 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.
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.
(Only available at rcsb.org/3D-view)
The Import Panel (Figure 20) 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 20B). 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 20B). The identifiers of multiple structures can be listed at once by separating them with commas (Figure 20C). After the identifiers have been inputted, click “Apply” to upload the structures.
(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 21A).
- Deleting/Replacing Views: The Views menu contains a list of all saved views. Next to each view is a trash can icon (Figure 21B). 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 21 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 21: Options to A. create, B. delete and C. view sessions.|
(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 22) will appear in the Controls Panel next to the 3D canvas.
Superposing by Chains: In order to superpose structures by chains (Figure 23), 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.
|Figure 23: A. Select option for Superposition by Chain; B. Select polymer chains for superposition and then click on Superpose.|
Superposing by Atoms: In order to superpose structures by atoms (Figure 24), 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.
|Figure 24: A. Select Superposition by Atoms; B. Select atoms for Superposition and then click on Superpose.|
Note: Explore the Pairwise Structure Alignment tool for another option for superposing 3D structures.
- 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., “Assessing PDB Macromolecular Crystal Structure Confidence at the Individual Amino Acid Residue Level”, 2022, Structure (accepted)
- 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