Pcmodel Main Window

The main window consists of the Menu bar, the Draw Tools bar, the molecule window and the templates window.

The Molecule Window shows all the atoms currently known to Pcmodel. Atoms may be placed into the Molecule window using the Draw and Build options from the Draw Tools or by reading a file of atoms using the File Menu or one of the builder templates from the Templates Menu (Rings, Amino Acids, Sugars, Nucelosides, OrganoMetallics, Heterocycles, Solvation). The type of display is controlled by options in the View Menu (stick, tubes, ball and stick, labels). Manipulation of the atoms is done with the mouse (left button for rotation, right button for translation, center wheel for zoom – see below for more information).

The Template window is a work area for various dialogs. The default template is a set of Atom Type buttons that allows you to change the atom type of one or more atoms. Select the Atom Type and then click on the atom(s) to change using the left mouse button. Other templates include builders for Peptides, Sugars, and Nucleosides, list of Heterocycles and Organometallics, controlls for Molecule Orbital and IR Spectra display, crystallography information, and a Property Display of the current structure. The Template Window is also used to display information during an Energy Minimization or Conformational Search.



Mouse Controls

Pcmodel assumes a three button mouse. The X axis is left to right, the Y axis is bottom to top and the Z axis is out of the plane of the screen.

Rotation in X and Y: Left Mouse Button,

Rotation in Z: shift key and Left Mouse Button

Translation: Right Mouse Button

Zoom: Center Mouse Button or Wheel

Select an Atom: Click on the atom with either Left or Right Mouse Button

Select a Molecule: Double click on an atom. This assumes there is more than one molecule in the Structure Window and Pcmodel knows they are distinct molecules. Use Find Molecules from the Molecule Menu to make distinct molecules. Use Clear Select Molecule to unselect all molecules.

Single Button Mouse and Macintosh Trackpad:

Rotation: click and drag

Translation: Apple Key with click and drag

Zoom: two finger drag