Overview

Main Window

The main window of IQmol is partitioned into four main parts:

  • The Tool Bar provides access to common functions.
  • The Model View provides a hierarchical view of the data structures that make up the system.
  • The History view displays the actions that can be undone. Clicking on the item in the list will take the system back to that state. The Edit→Undo and Edit→Redo menu options can also be used to navigate the history stack. The number of undo operations can be configured in the preferences.
  • The Viewer forms the main part of the window and is where the molecule is is displayed.

Opening Files

IQmol's file IO is handled by the OpenBabel libraray which can handle many common chemical file formats including the following:

Type File Extension
XYZ coordinates .xyz
Q-Chem input/output .inp/.out
MDL Molfile .mol
Protein data back .pdb
Chemical markup language .cml
Formatted checkpoint files .fchk

Check the OpenBabel documentation for other supported file types.

Files can be opened using the menu File→Open or the Tool Bar button. Additionally, multiple files can be opened using the command line or, on systems that support drag and drop, by dragging the file icons from the system file manager into the Viewer window.

Note that when opening multiple files, only the last one is displayed. Use the checkbox associated with each molecule to toggle its visibility.

Building Molecules

By default, IQmol opens in build mode. This is indicated by a red border around the icon in the Tool Bar. Clicking in the empty Viewer window will create an atom of the type indicated by the Build Element button next to the Build button in the Tool Bar. Clicking the Build Element button causes a pop-up periodic table to appear, from which a new build element can be selected.

Additional atoms can be added by clicking on an existing atom and dragging the mouse. This creates a new atom bonded to the first. To create a separate fragment, hold down the alt modifier key when clicking in the Viewer window.

Bond orders can be increased by clicking and dragging between two existing atoms. If no bond exists between the two atoms, one is created. Otherwise the bond order is increased. To decrease the bond order, the bond must first be deleted and a new bond created.

Entire frgaments can be loaded from an existing file by using the Tool Bar button.

IQmol operates in free-form mode, which means standardized bond lengths and angles are not used. It is recommended that after drawing a moleule an energy minimization is performed using the Tool Bar button. Note that if your initial structure is very poor, the minimizer will start off with too much energy and may not converge to the desired structure. Performing an additional minimization should fix this.

If your molecule is symmetric, the optimizer is unlikely to find a structure with the desired symmetry. If this is the case, a nearly symmetric structure can be symmetrized using the Build→Symmetrize Molecule menu option. Finding very high symmetry may require relaxing the tolerance using the Build→Set Symmetry Tolerance menu option.