The 3D viewer implemented in Makya 3D is Mol*. More information can be found in the Mol* documentation (here).
Functions of the Toggle Menu, from Mol* Viewer Documentation. David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; 10.1093/nar/gkab31.
As described in the Mol* documentation:
"All the interactions with the molecule(s) uploaded in Mol* require using mouse controls (in the 3D canvas). These controls allow the user to manipulate the display of structures via a variety of functions such as rotating, translating, zooming, and clipping the structures. When not specified, a “click” refers to pressing the left mouse button (or tapping a single finger on a touchscreen). If an action is available for the right mouse button, it can also be performed by using the Control button + left mouse click. The general mouse controls are listed below:
- Rotate - Press the left mouse button and move, or use the Shift button + left mouse button and drag.
- Translate - Press the right mouse button and move, or 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 touch pad, 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 see.
- Change clipping planes - Use the Shift button + the mouse wheel. On a touch pad, use the Shift button + a two-finger drag.
Moving the mouse over (or hovering over) any part of the 3D structure displayed in the 3D canvas, without clicking on it, will highlight it (by coloring it in magenta) according to the Picking Level currently selected. Additionally, in the lower right corner of the 3D canvas, information about the PDB ID, model number, instance, chain ID, residue number, and chain name of the highlighted part is listed.
As you interact with the structure using the mouse, Mol* allows two modes for which the behavior of a click is different. As a result, each mode lets the user perform unique operations. To switch between the two modes, use the Selection Mode icon (shaped like a cursor) that appears in the Toggle Menu. The list below summarizes the functionalities of the Default Mode and Selection Mode.
- Default Mode: A click on a residue (or any object in 3D) will focus on it. The focused residue and its surroundings (residues and ligands) 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.
- Selection Mode: A click on a residue (or any object in 3D) will select it. What exactly is selected depends on the value of the Picking Level. Selected parts of the structure will appear with a bright green tint in the 3D canvas and in the Sequence Panel. 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. Clicking on any point in the 3D canvas that has no atom will clear the selection.
Selection Mode allows parts of 3D structures to be selected by clicking on them. It also allows residues to be selected through Set Operations Menus. Selection Mode is enabled by clicking on the cursor icon in the Toggle Menu. Activating Selection Mode opens a toolbar that appears at the top of the 3D canvas."
The functionalities present in the Selection Mode toolbar are described further in the Mol* documentation.
Visualization of interaction weights
In the visualization, you will notice spheres on certain atoms that grow or shrink as you change interaction weights. These spheres represent the weight of each interaction. When an interaction involves a ring, spheres will appear on all necessary atoms. Dash lines are colored by interaction type; when hovering over the dash lines, you can see additional information related to the interaction types and involved atoms.