Picking Modes
You have already seen that VMD can label individual atoms by
simply clicking on them with the mouse. In addition, VMD supports
several other picking modes. For a listing of them, hold down the
rightmost mouse button in the GL Display to reveal the
popup menu. Drag down to the Pick Item Mode submenu. By default,
VMD is in the "Query" mode, allowing you to pick atoms and display
labels. If you switch to "Center" mode and choose an atom in
the display, then subsequent rotations will be performed about this
atom position. In essence you will have picked a new center of
rotation. Another useful picking mode is "Bonds." If you select
this option and click on two atoms in the display window, a dashed
line will be drawn between them and the distance separating them
will be calculated. To familiarize yourself with this option,
try clicking on two atoms of the bR retinal residue. Choose
one atom from the segment which remains in the binding pocket,
and the second atom from the cleaved portion which is pulled
outward. If you then animate the system, you will see how the
distance between the two retinal pieces increases over the course
of the simulation. If you would like a graph of this distance
over time, try this: hold the rightmost mouse button down
in the GL Display window. Drag down to "Show Form" in the
popup menu and choose "labels". In the
upper left corner of labels, change the Category to Bonds. Click on
one of the entries which appears in the blue browser window and
hit the "Graph" button. A plot of the bond length over the course
of the simulation will appear.
Similar in spirit to the "Bonds" picking mode are "Angles" and
"Dihedrals." In these modes, you should click on three or
four atoms respectively to calculate the angles defined by those
collections of objects.
Finally there are the Move options. If you choose MoveAtom and
select an atom in the display window, you will be allowed to
drag it about the screen to change its position. For instance,
suppose you wanted to refine a bond length by hand in VMD. One
would first choose the "Bonds" picking mode and calculate the
distance between the two atoms forming the bond. Then you
would select "MoveAtom" and drag one of the atoms to the
desired bond length. The distance will be updated and displayed
on the screen automatically. A similar strategy could be used to
modify bond or dihedral angles by hand.
When one does a lot of picking in VMD, the display tends to get
cluttered. You can selectively delete output from picking actions
by using the popup menu's "Labels" option.