How to navigate

• Rotate the view in the active cell by pressing the left mouse button and drag the mouse.

• Zoom by dragging while pressing the middle button or by left-dragging while the Alt button is pressed.

• Translate by holding down the right mouse button and dragging or by left-dragging while the Shift button is pressed.

• Bring up the Popup Menu by clicking with the right mouse button.

• Set the center of transformation by middle click on a component

• If there are more cells, activate a cell by clicking it once. The active cell has a red border, and navigation will perform in the active cell.

  Starting navigation in an inactive cell activates the cell.

  Navigation will take effect in every cell when Synchron mode is checked in the Layout menu.

• Navigation keys can be changed by selecting the Display ->Options menu and selecting the Controls tab on the appering dialog.

• Zoom can also be inverted by the Options dialog, so that dragging the mouse up will take the view farther instead of bringing it closer.

How to use the Selection Panel

• Hiding and showing components can be done quickly by clicking on their image in the Selection Panel.

• Further display settings can be accessed by right clicking on a node.

How to use Drag & Drop

• Molecules can be moved from MarvinSpace to other applications if the Selection Panel is available. Clicking on a molecule node of the Selection Panel and holding down the mouse button allows dragging.

• Molecules from other applications can be dropped to MarvinSpace.

How to use monitors

• Measure distance by clicking the first icon on the Toolbar, and selecting two components afterwards.

• Measure angle by clicking the second icon on the Toolbar, and selecting three components afterwards.

• Measure dihedral by clicking the third icon on the Toolbar, and selecting four components afterwards.

• To measure again the buttons on the Toolbar have to be pressed again.

• Selected components will loose selection after pressing any of the measure buttons.

How to change dihedral

1. Measure the dihedral

2. Click on the green arrowed circle of the appearing dihedral monitor

3. Press and hold down the Ctrl button while left-dragging the mouse

How to use controls (translate, rotate, resize)

1. Select e.g. a small molecule in the Selection Panel: click on it with the left mouse button

2. Click the right button to get the Popup Menu

3. Choose the first item, Select, so that atoms of the selected structure become highlighted

4. Now press the Translate control button in the toolbar

5. Drag the selected object: hold down the left mouse button plus press the Ctrl (control) key on the keyboard and move the mouse

Rotate and Resize can be used the same way. Note that each controls may not be allowed to each components, for example a molecule cannot be resized, or a molecular surface cannot be translated or rotated without translating or rotating the molecule itself.

How to restict the view to a binding pocket

There are several ways to do that:

• The easiest when you have a macromolecule loaded that has one ligand, just bring up the Popup Menu, and select the Zoom to pocket option.

• You can do this manually with lots of other options to customize:

  1. Choose a ligand on the Selection Panel, and bring up its Popup Menu

  2. The Select neighborhood will have every component that is closer to the ligand than 2 Angstroms to be selected.

  3. Polymers have the option in their Popup Menu to Extend the selection to residues

  4. Now you may wish to select or deselect components manually

  5. Bring up the main Popup Menu by right clicking on the canvas

  6. Select either the Hide unselected components or the Fade unselected components option.

How to create molecular surface of a binding pocket

1. Restrict the view to the binding pocket

2. Create the molecular surface by the Show Surface menu in the main Menu Bar

3. Select the molecular surface through its Popup Menu in the Selection Panel, and a bounding box will appear

4. Select the Resize control option in the ToolBar

5. The bounding box can be considered as six clipping planes, and the resize control will change the size of the bounding box

6. The bounding box can also be translated with the Translate control option.