Using Mol*¶
Structure Viewer¶
The Structure Viewer is the main component of Mol*. It displays the 3D structure of the molecule(s) in the PDB file(s) that are currently open. It is located in the center of the screen.
Mouse controls¶
- Rotate: click the left mouse button and move. Alternatively, use the Shift button + left mouse button and drag to rotate the canvas.
- Translate: click the right mouse button and move. Alternatively, use the Control button + the left mouse button and move. On a touchscreen device, use a two-finger drag.
- Zoom: use the mouse wheel. On a touchpad, use a two-finger drag. On a touchscreen device, pinch two fingers.
- Center and zoom: use the right mouse button to click onto the part of the structure you wish to focus on.
- Clip: use the Shift button + the mouse wheel to change the clipping planes. On a touchpad, use the Shift button + a two-finger drag.
- Highlight: hovering over any part of the 3D structure displayed in the Structure Viewer, without clicking on it, will highlight it (by coloring it in magenta) according to the current Picking Level. Additionally, in the bottom right of the Structure Viewer, information about the PDB ID, model number, instance, chain ID, residue number, and chain name is listed for the highlighted part of the structure.
- Focus: In default mode, click on a 3D object to focus on it. The focused object and its surroundings will be displayed in a ball & stick representation. All local non-covalent interactions will be shown. To hide the surroundings, click on the target residue again. To un-focus, click on any point in the Structure Viewer that has no atom.
Toggle Menu¶
This menu provides users quick access to some commonly used operations for the Structure Viewer. It is located towards the right side of the Structure Viewer and has the following functions.
Function | Description | Icon |
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Reset Camera | Centers and resets the view of the structure on the Structure Viewer | |
Screenshot/State Snapshot | Takes an image of the structure as shown and gives options for resolution and download | |
Controls Panel | Hides/shows the Controls Panel to the right | |
Expanded Viewport | Expands Structure Viewer and Controls Panel to the full browser screen | |
Settings/Control Info | Provides settings for viewing of Structure Viewer, as well as information about moving in 3D and mouse controls | |
Selection Mode | Switches between Default Mode and Selection Mode |
Selection mode¶
You can enter the Selection Mode by clicking on the "" icon in the Toggle Menu.
In selection mode, a click on a residue (or any object in 3D) will select it (instead of focus it in the default mode). What exactly will be selected depends on the value of the Picking Level. Selected parts of the structure will appear with a bright green tint both in the Structure Viewer and in the Sequence Viewer. Clicking on any point in the Structure Viewer that has no atom will clear the selection.
When selecting polymers with the Picking Level set to “Residue”, holding the Shift key while clicking will extend the selection along the polymer from the last clicked residue on. One could also press, drag along the polymer sequence and release in the Sequence Viewer to select multiple residues.
Activating Selection Mode opens a toolbar that appears at the top of the Structure Viewer. The following provides an illustration of the toolbar and a description of each of the buttons:
Function | Description | Icon |
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Picking Level for Selecting and Highlighting | Controls to what level a selection or highlight interaction is applied (i.e., atom, residue, chain, etc.) | |
Add/Union Selection | The new selection will be the union of the current and the other selection | |
Remove/Subtract Selection | The new selection will be the current selection with parts that are in the other selection removed | |
Intersect Selection | The new selection will be the intersection of the current selection and the other selection | |
Set Selection | The new selection will be the other selection | |
Apply Theme to Selection | Enables changes of color, transparency and clipping to be applied to the current selection | |
Create Component of Selection with Representation | Enables components to be created and its representations to be changed independent of other components | |
Remove/Subtract Selection from All Components | Removes the current selection from being displayed in the Structure Viewer | |
Undo Modify Selection | Allows certain actions (changes of color, hiding of components, etc.) to be reverted while remaining in the selection mode | |
Show/Hide Help | Offers a summary of selection operations, representation operations, and mouse controls | |
Turn Selection Mode Off | Switches from Selection Mode to Default Mode |
Picking Level¶
The Picking Level controls to what level a selection or highlight interaction is applied. Specifically, a selection/interaction can be extended from a single atom to a residue (default), chain, entity, model, or structure. For example, if you click on an atom on the Structure Viewer and the picking level is set to "chain", you would end up selecting the whole corresponding chain of that atom. If the structure contains symmetry instances and the picking level ends with "instances" (e.g. "chain instances"), the interaction would be extended to include all atom / residue / chain instances of the clicked atom.
In addition, the picking level determines the specificity of a selection in the Sequence Viewer, or the specificity of the focus in Default Mode.
The Picking Level can be changed via a menu in the Selection Mode toolbar located at the top of the Structure Viewer.
Create a Component from Selection¶
Under selection mode, we can create a new component from selections. Creating components allows the user to make groupings of certain parts of a structure for subsequent manipulation (see Actions on Components). For example, if you want to visualize a protein and its ligand separately, you can create a component of the ligand and hide it. Then you can change the representation of the protein without the ligand being in the way.
You can create a component by clicking on the "" button, located in the Selection Mode toolbar at the top of the Structure Viewer. A menu will appear, where you can fill in the following parameters:
- Selection: the selection to be used to create the component. Defaults to the current selection. You can also use a new selection that consists of, e.g. a certain amino acid type (by selecting "Amino Acid > Alanine (ALA)", for example), or all surrounding residues of the current selection (by clicking "Manipulate Selection > Surrounding Residues (5Å) of Selection").
- Representation: the representation to be used for the component. Defaults to None.
- Options:
- Label: label of the component. Defaults to "Label".
- Check existing: checks if a selection with the specifield elements already exists to avoid creating duplicate components. Defaults to false.
Once you click on "Create Component", the component will be created and displayed in the Structure Objects panel. You can now perform actions on the component.
Example: extract antibody chains from a complex structure and save it¶
If you would like to extract the antibody chains from an antibody-antigen complex structure and store them to another file, you can follow the steps below:
- Import the complex structure file from cloud or upload it from your local machine. Open the file by clicking the file name in the Files & Jobs panel.
- Open the selection mode by clicking the "" button on the right of the Structure Viewer.
- Change the picking level to "Chain", then click on the chains of the antibody to extract.
- Create a component named "antibody" by clicking the "" button on the top of the Structure Viewer.
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Save the component to a CIF file in the project by clicking the "antibody" component in the Structure Objects panel and then clicking "Save" in the dropdown menu. Enter the file name to create and click "√".
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Now there will be a new CIF file in the Files & Jobs panel.
Sequence Viewer¶
The Sequence Viewer displays the polymer sequences of macromolecules (proteins and nucleic acids) present in the PDB structure(s). In addition, it provides quick access to any small molecular ligands or entities present in the structure(s). It is located at the top of the screen above the structure viewer.
The Sequence Viewer contains several drop-down menus that allow the user to choose which sequnece to display:
- Structure: select which structure to display.
- Mode: select between three display modes: chain, polymers and everything. In the chain mode, each chain is displayed as separately. In the polymers mode, all polymers are displayed together. In the everything mode, all entities are displayed as together.
- Entity (only in chain mode): select which entity to display.
- Chain (only in chain mode): select which chain to display.
On the top-right of the panel, there are four buttons:
- (Copy to Clipboard): Copy the displayed sequence to the clipboard. Currently, this is only displayed when the display mode is set to "chain".
- (Wrap sequence): Wrap the sequence to fit the width of the panel. If disabled, the sequence will be displayed in a single line. Defaults to true.
- (Secondary Structure Annotation): Display the secondary structure annotation of the sequence. Alpha helices in the sequence are wavy-underlined, and beta sheets are straight-underlined. Defaults to false.
- (CDR Annotation): Display the CDR (complementarity-determining region) annotation of the sequence. Defaults to false. When clicked, a menu will appear where you can select which CDR definition to use from "IMGT", "Chothia", "Kabat" and "North". The corresponding CDR residues will be underlined.
Structure Objects¶
Structure objects are 3D objects displayed in the Structure Viewer. They can be accessed via the Structure Objects component, located at the bottom-left of the Project Editor. The Objects component contains a list of files that are currently open (i.e., has a light blue background in the Files & Jobs panel). Each file is displayed in a tree-like structure, with the following hierarchy:
Structure Hierarchy¶
- Raw data: the raw data of the file, usually a PDB or mmCIF. This may not be present if the file is imported from cloud.
- Trajectory: a collection of models that represent the temporal (time-serie) or ensemble variation of the structure. This is the top level of the parsed structure.
- Model: a frame in the trajectory that contains structural information of some molecule(s). You can switch between different models in a trajectory by clicking on the trajectory -> "Update Molecular Model" and selecting the model you want to display.
- Structure: a structure is a collection of units. Generally, a single unit corresponds to a single chain, with the exception of consecutive "single atom chains" with same entity_id and same auth_asym_id, e.g. water molecules.
Constructing the root structure¶
The root structure is itself a hierarchy of components or sub-structures. Given proper annotation in the mmCIF/PDB file, you can construct the root structure from a model via multiple ways.
- Model: Creates a structure purely based on the atomic coordinates and bonding information available in the model, without considering any higher level organization from the crystallographic assemblies.
- Assembly: Creates a structure based on the user-selected assembly of the macromolecule. In the context of a crystal structure, the atomic unit cell is built up by applying symmetry operations to the asymmetric unit to create a crystallographic assembly.
- Symmetry: Creates a structure by applying a user-defined symmetry operation, which includes translation, rotation, or mirror operations, to the asymmetric unit.
- Symmetry Mates: Creates a structure by finding symmetry mates within a certain radius. Symmetry mates are images of the asymmetric unit created by symmetry operations.
- Symmetry Assembly: Uses defined symmetry operators and asymmetric units to construct a custom biological assembly.
- Auto (default): Creates a "model" structure if there are no available assemblies. Otherwise, defaults to the first assembly.
You can change how the root structure is constructed by clicking on it -> "Update Structure" and selecting the desired structure construction method.
Structure Representation¶
Represention of a structure determines how the structure is displayed in the Structure Viewer. The following representation types are available:
- Cartoon: Displays ribbons, planks, tubes smoothly following the trace atoms of polymers.
- Backbone: Displays polymer backbone with cylinders and spheres.
- Ball & Stick: Displays atoms as spheres and bonds as cylinders.
- Carbohydrate: Displays carbohydrates as symbols (3D SNFG).
- Ellipsoid: Displays anisotropic displacement ellipsoids of atomic elements plus bonds as cylinders.
- Gaussian Surface: Displays a gaussian molecular surface.
- Gaussian Volume: Displays a gaussian molecular density using direct volume rendering.
- Labels: Displays labels for atoms, residues, and chains.
- Lines: Displays bonds as lines and atoms as points or croses.
- Molecular Surface: Displays a molecular surface.
- Orientation: Displays orientation ellipsoids for polymer chains.
- Point: Displays elements (atoms, coarse spheres) as points.
- Putty: Displays a tube smoothly following the trace atoms of polymers.
- Spacefill: Displays atomic/coarse elements as spheres.
- Non-covalent Interactions: Displays non-covalent interactions as dashed cylinders.
- Validation Clashes: Displays clashes between atoms as disks. Data from wwPDB Validation Report, obtained via RCSB PDB.
- Membrane Orientation: Membrane Orientation calculated with ANVIL algorithm.
Besides the representation type, there are two key parameters that determine how the structure is displayed: color theme which determines the coloring, and size theme which determines the size of the representation.
Structure Representation Presets¶
The default structure representation determines how the root structure is split into components and how each component is displayed by default. The decision for representation happens in two major steps:
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Size Determination: The size of the structure is classified into five categories: Small, Medium, Large, Huge, and Gigantic.
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A structure with a residue count less than 10/5000/30000 is considered "Small", "Medium" and "Large", respectively.
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If a structure has a > 30000 residue count, it is categorized as "Huge" if it has a high symmetry unit count; otherwise, it's "Gigantic".
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Representation Selection: Based on the size determined, an appropriate representation is chosen. The logic is as follows:
- Small: Use the AtomicDetail display with carbohydrate symbols.
- Medium: If the residue : gap ratio is greater than 3, use the PolymerAndLigand display. If it's less, display in the same way as "Small".
- Large: Use a PolymerCartoon display where the ligands are not displayed.
- Huge/Gigantic: Use the CoarseSurface display, which helps show structures of this size without overloading the system.
The automation here helps provide an optimal view of the molecular structure based on its size and complexity, essentially balancing detail and performance.
Actions on Components¶
The following actions can be performed with components:
- Show/Hide the component via the "/" button.
- Delete the component via the "" button - this will remove the grouping but the structure will remain intact.
- Update the representation by clicking "Apply Action" -> "Update 3D Representation" and then selecting the desired representation type, color theme, and size theme.
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Modify the content of the component by the current selection by clicking "Apply Action" -> "Modify by Selection" and then selecting one of the following operations:
- Include: The new component will be the union of the current and the other component.
- Subtract: The new component will be the current component with parts that are in the other component removed.
- Intersect: The new component will be the intersection of the current component and the other component.
- Edit the label of the component by clicking "Apply Action" -> "Edit Label" and then entering the new label in the text box.
- Save the component as a file in the project by clicking "Apply Action" -> "Save" and then entering the desired file name in the text box.