Mouse operations in InsightII:

Rotating or translating a whole molecule

• Note: to insight, all the coordinates in a PDB file are considered part of the same molecule, including multiple polypeptides, cofactors, and water molecules.  They will all rotate or translate together.
• Right click and drag to rotate in any dimension.
• Use left and right mouse buttons together to specifically rotate around the z axis.  If the result seems confusing, try a series of straight horizontal or vertical strokes.
• Middle click and drag to translate in the x or y dimension.
• Use left and middle buttons together to translate in the z dimension.
• You may alternatively use the "dials" (sliders in the box on the lower left) to conduct specific rotations or translations.

Scaling

• Use the middle plus right mouse buttons to expand or contract the scale of the display.  There is also a "dial" for scaling.

Adjusting the "slab"

• The slab is the slice of vertical coordinates that is displayed.  Positioning of the slab boundaries affects how color intensity is used to give depth cues.  The best way to adjust the slab is to use the "side view" icon from the left margin.  In the side view window, the slab boundarys can be directly dragged into position.  Alternatively, one of the "dials" is flip-flopped between controlling slab position and slab thickness by the button on the far bottom right, or by pressing function key F12.  However, there is a mouse operation that can change the slab thickness or position.
• Pressing all three mouse buttons and dragging changes slab position or thickness.
• F12 changes the meaning of the mouse operation the same way it changes the meaning of the "dial".
• If the results of this operation seem confusing, try it while the side view window is activated.

Rotating, translating, or scaling with two or more molecules on the screen:

• This situation would primarily arise after two pdb files had been loaded and aligned to each other.  The two objects can be either translated and rotated in coordination, or they can be translated or rotated individually.
• To translate or rotate all objects in coordination, click <connect to world> (on lower button bar) or press function key F11 prior to the operations listed above.
• To translate or rotate an individual molecular object (meaning the contents of one PDB file) click <connect to object> or press function key F10 prior to the operations listed above.
• <Control middle> or <control right> mouse click and drag will automatically connect only to the clicked upon object.
• However "connect to object" is specified, it cancels "connect to world" for subsequent operations.
• "connect to object" or "connect to world" modes also affect the operation of the "dials".

Selecting parts of a molecule to change its appearance.

• There are many options in the pull down menus  to change the appearance of parts of the displayed molecule (color, display or not, render, apply ribbon, etc.).  Color  (activated from <molecule><color>) will serve as an example of mouse operations related to specifying subsets of a molecule to alter.
• After <molecule><color> a window pops up in which a set of atoms or residues may be explicitly typed in the "molecular specification" field.  Alternatively, the subsets to be colored may be specified by mouse clicks either before or after opening this window.

Prior selection of atoms/residues to color:

• This is preferable to the method below because you have a chance to review your selection before committing to it.  However, trying to build up a complex selection with mouse clicks this way is frustrating because you may easily inadvertantly cancel your partially defined selection.  Alternatively, consider using <subset><define> to define one or more named subsets, and then applying color to them by subset name in the <molecule> <color> window.
• If ATOM_SELECTION is typed in the molecular specification box, then whatever was selected prior to activating the <molecule><color> window will be colored upon clicking <execute>.

Prior to activating the <molecule><color> window:

• Left clicking on an atom will select it.  Appearance of selected atoms is altered, although depending on the style of rendering you may have to look closely to see the difference.  The message box names atoms (or residues) upon selection.
• A <beep> means there were overlapping atoms; check the message box to see that you got the one you intended.
• Left clicking on a bond automatically selects both bonded atoms.
• BE CAREFUL not to hold the mouse down for 2 seconds when left clicking, else you activate a routine to move the selected atom.  This is signaled by change in the cursor appearance to orthogonal arrows.
• Double left clicking on an atom will select the whole residue.
• Alternatively, the "selection_level" icon along the left margin can be used to set a left mouse click to select among single atoms, whole residues, or the whole molecule.
• If "whole residue" is set, then double left clicking gives "whole molecule" selection.
• If "atom selection" is set, then clicking on a bond selects both bonded atoms.
• If "whole residue" is set, then clicking on a peptide bond selects both adjacent residues.
• A <shift left click> will add or subtract from an existing selection.
• A left click elsewhere cancels a selection.
• You may left click and drag to draw a box to select a range of atoms.
• You may <control left click> and drag to draw a lasso around a range of atoms to select them.
• Holding down <shift> while drawing a box or lasso causes the new selection to either add or subtract from the pre-existing selection.  Note: those atoms in the drawn box not already in the selection will be added, while those already in the selection will be subtracted at the same time.
• Box or lasso drawing with atom_selection in force will only select displayed atoms.  For example, if you have chosen to only display CA atoms (by <molecule><display><*:*:CA>), then then only CA atoms in the box are selected.
• Atoms that are in the box but not in the slab are not selected.
• Box or lasso drawing with residue_selection in force will select all atoms in any residue that has one displayed atom in the box.

Selection with the mouse after the <molecule> <color> window is open.

• Consider saving a folder prior to using this method, especially if you have a complex pattern of colors already established.  It is easy to overwrite the coloring of large unintended sections of the molecule, and there is no convenient way to undo the damage.
• The items to be colored are affected by the setting in the "molecular pick level" window that co-opens when the "molecular specification" box is highlighted.
• As before, one can set a left mouse click to select individual atoms, whole residues, or the whole molecule.  BE CAREFUL - the default is "whole molecule".
• An additional possible selection is "subset".  These may be subsets of atoms predefined in the pdb file (eg. helixA, helixB, etc.).   Alternatively, you may create your own named subsets with the <subset><define> command.
• Rather than trying to select the subset by clicking in the main window, you may select it from the list box that appears when the subset radio button is checked (turns yellow).  BE CAREFUL - the subset is colored immediately when you click on the name in the list box.
• Similarly, if "molecule" is set for "molecular pick level" and you click on a molecule object name in the list box, the whole molecule is immediately colored.
• If the mouse is moved over the main display while the <molecule><color> window is open, the cursor will change to a cross-hair indicating that whatever is left clicked next will be colored.
• If nothing happens, it is probably because the color field has not yet been filled in, or there was nothing under the cross-hair.
• Only left clicking works, and there is no box or lasso drawing allowed.
• It always beeps.
• Each item is immediately colored upon being selected.  You may select and color additional items as you wish.  There is no convenient way to undo such a color operation.  You can either explicitly recolor it the way it was before, or use the "replay log" function to start from the beginning and work up to the point prior to the error.

Using the mouse to move selected parts of the molecule.

• To translate a selected subset of the molecule relative to the remainder:
• First select all atoms to be moved.
• Then left click and hold over one of the selected atoms.  When the cursor changes to a cross-hair of orthogonal arrows (~ 2 sec.), you may drag the selection to a new position.  Any bonds connecting the dragged segment to the rest of the molecule will stretch as necessary.  BE CAREFUL - there is no convenient way to undo this operation.
• To rotate a selected subset around a bond:
• Select the two atoms on either side of the bond to be rotated.
• Select the torsion icon from the left margin.
• Wait for the bond to be annotated with a cone.  In Insight terminology, the cone and associated bond angle label is called a "torsion monitor".
• If you note down the initial bond angle, then you can correct an error by just rotating back to the initial number.
• The fat end of the cone is towards the section that will rotate.  If you wish the other section to rotate, then left click on the bond.
• Middle click on the cone and drag to rotate.
• If you click elsewhere, the bond will be temporarily deactivated and the cone will disappear.  To reactivate it, left click on the bond.  The bond angle label will remain to show the positions of multiple bonds that can be activated to rotate.
• If there are multple objects loaded, the others will remain stationary during a torsion rotation even if "connect to world" is in effect.
• One can delete torsion monitors from the <transform><torsion> window.