The toolbar is located below the Protean 3D menus, and can be shown or hidden using the Controls > Show/Hide Toolbar command. The first two tools on the left of the toolbar affect the entire Protean 3D project, while the remaining tools affect only the Structure view. See that topic for a video demonstrating those tools.

The Structure view tools can either be “sticky” or “transient,” as color-coded in the table below.

  • Sticky – Protean 3D stays in the selected mode until you choose a different function.
  • Transient – The selected mode only stays active as long as you are actually using the controls.
Task How To
To open a file Press the Open a local file tool (). For information on the various options, see Open a file or project.
To save the document Press the Save to a file tool (), use File > Save, or press Ctrl/Cmd+S. The document is saved in .structure file format.
To rotate the molecule in any direction Use the Rotate tool (), press Structure > Rotate, or hold down the left mouse button and move the mouse in any direction.
To rotate the structure around the z-axis Use the Rotate Around Z-Axis tool (), use Structure > Rotate Around Z-axis press Shift+click, or hold down the left mouse button and move the mouse right to rotate in a clockwise direction; or left to rotate in a counter-clockwise (anti-clockwise) direction.
To move the molecule relative to the background Use the Move tool , use Structure > Move, press Alt+click (Win) or +click (Mac), or hold down the left mouse button and drag the mouse in any direction to move the structure the same way.
Note for the three rows above: If the molecule has 20,000 or more atoms, the side chains will temporarily disappear in the Structure view when you rotate or move the molecule. This circumvents slow-downs that would occur if the completely-rendered molecule was refreshed throughout the rotation or move. The side chains will appear again as soon as you stop rotating or moving the molecule.
To zoom in or out Use the Zoom tool (), use Structure > Zoom, use the mouse’s scroll wheel, or hold down the left mouse button and rag the mouse up to zoom in and down to zoom out.
To select neighboring residues Use the Select Neighbors tool (), use Structure > Select Neighbors, or press Shift+double-click.
To move a selection to the center of the screen and make it the center of rotation Use the Center on Selection tool (), use Structure > Center on Selection, or press Alt+double-click. Alt + double-click both selects an item and centers the selection on it.
To re-center and resize the model to fit in the view Use the Reset Structure View tool (), use Structure > Reset Structure View, or press Ctrl/Cmd+Shift+R.

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