Mouse Menu

The Mouse menu indicates and controls the behavior of the mouse when the mouse moves and clicks within the graphics window. Mouse clicks and drags can affect VMD in one of two ways. It can change the view of the scene, either by rotating, translating, or scaling. It can also pick objects in the scene, causing some further action to be taken. These behaviors are all reflected in the state of the Mouse menu.

Below, we describe the main parts of the Mouse menu.

Mouse modes

The top three menu items select whether the mouse will rotate, translate, or scale the scene when the user clicks and drags with the left mouse button.

Pick modes

These modes, located right below the mouse modes in the Mouse menu, control how the mouse affects objects in the scene (as opposed to how the mouse changes the view of these objects). Note that any time you choose a new pick mode, the current mouse mode changes to "Rotate".

• Center changes how VMD rotates and scales the scene. To get a feel for how this works, select "Center" from the Mouse menu, then click on an atom in the scene. If you now rotate the scene by clicking and dragging with the left mouse button, the scene should rotate about the picked atom. If you change the view mode to "Scale" using the "View Mode" pulldown menu, the scene will expand while keeping the picked atom in view. The picked atom will remain the center atom until a new atom is selected as "Center", the "Reset View" button is pressed, or a new molecule is loaded.

• Query prints information about the item (e.g. the atom name) on the text console window.

• Label adds labels to atoms in the scene. Labels include atoms, bonds, angles, and dihedrals. These labels require, respectively, one, two, three, and four atoms to be picked. For the latter three label types, the numerical value of the geometric label is displayed, along with a stippled line connecting the picked atoms. The units for "Bonds" corresponds to whatever units the coordinate file is written in. "Angles" and "Dihedrals" are measure in degrees.

  Labels can then be manipulated through the Labels form.

• Move changes the actual coordinates of atoms in the scene. Note that this is different from simply changing the view. Clicking on one of the buttons in the Mode Mode menu selects what group of atoms to move. "Atom" moves only the selected atom. "Residue" moves all atoms in the same residue (e.g., amino acid or nucleotide) as the selected atom. "Fragment" moves all atoms connected by a bond to the picked atom. "Molecule" moves every atom in the molecular structure. "Highlighted Rep" is the most flexible; it moves all atoms in the highlighted representation in the browser window of the Graphics form.

  Atoms are moved by clicking and dragging with the left mouse button. If the shift key is held while the mouse is moved, the affected atoms are rotated about the selected atom. Rotating atoms with the left button rotates about the x or y axis of the screen; rotating with the middle or right button rotates about an axis perpendicular to the screen.

  Note that there is currently no way to undo Move operations, so the atom coordinates should first be saved to a file.

• Force applies a force to selected atoms in a running simualtion. These forces will be visible only if an IMD connection has been established. Clicking and dragging with the left mouse button will apply a force to the selected Atom, Residue, or Fragment, as in Move Mode. Clicking with the middle or right button will cancel the force on the selected atoms.

• Move Light allows the lights to be positioned around the scene. Individual lights are turned on or off in the Display form. Selecting one of the lights in the Move Light menu rotates the selected light about the origin. The Move Light Mode can also be cancelled by changing into any other pick mode or mouse mode.

• Add/Remove Bonds adds a bond between two clicked atoms if there is not one present, and removes the bond otherwise. Both atoms must belong to the same molecule.