User`s guide

2. Building Molecules
Some file formats lack bonding information or do not correctly indicate multiple bonds. In such
cases, check the Generate Bonds box for WebMO to automatically generate bonds of the
imported structure using simple distance relationships. It is wise to then check the structure and
possibly open the editor to make any necessary changes.
When importing a molecule, it is possible to skip the step of saving the structure to the local hard
disk. Simply copy and paste the structure information into the textbox in the Import Molecule
page. The pasted text may be edited prior to clicking the Import Molecule button.
Structures from Previous WebMO Jobs
Sometimes one wishes to perform a calculation on the result of a previous WebMO job. For
example, to compute the infrared spectrum of a molecule, one first optimizes the geometry of the
molecule and then computes the vibrational frequencies of the optimized structure.
From the WebMO Job Manager page, scroll to the previous job, and click its View button
(
). Near the top of the results page is a picture of the previously computed molecule. Click
the New Job Using This Geometry button (
) under the
molecule. The Build Molecule page is opened displaying the molecule in its previously computed
geometry. Do not open the WebMO Editor (unless you wish to modify the geometry). Simply
proceed to the Choose Engine step (or Job Options step if only one computational engine is
available).
If desired, the displayed molecular geometry can be verified prior to running a job by clicking the
Select button (
). Select two, three, or four atoms by clicking the first atom and shift-clicking
subsequent atoms. The corresponding bond length, bond angle, or dihedral angle is reported on
the status line. When investigating the geometry of a molecule, it may be useful to reorient the
displayed molecule, which can be done by clicking the rotate (
), translate ( ), or zoom ( )
buttons and the dragging the molecule appropriately with the mouse.
B. WebMO Editor
WebMO contains a built-in 3-D molecular editor to create molecular structures for use in
subsequent calculations.
From the WebMO Job Manager page, click the Create New Job button (
) near
the bottom of the page to reach the Build Molecule page. Click the Open Editor button
( ) to invoke the 3-D WebMO molecular editor. The WebMO Editor opens in a
separate window.
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