When licensing Spartan via access code, choose 'Software Key' during the installation process:

• Follow the prompts to complete program installation
• Software Activation - Enter the 21 digit activation code and choose 'Activate' for on-line activation - This will activate your software
• If your computer does not have internet access, or if you have a strong Firewall, you may need to activate offline - In this case after entering your activation code, click on the 'Offline' button. Select (click on) 'Write Request File' - you will be prompted to specify a location to write a 'Request.txt' file. Email this 'Request.txt' file to codes@wavefun.com
• Within 24 hours, you will receive a response file named 'Request_code.txt' - Save this to your Desktop
• Open Spartan - When prompted for activation enter your 21-digit activation code (again)
• Click on the 'Offline' button, and this time choose 'Activate From File' - point the resulting dialogue to the 'Request_code.txt' file on your desktop
• This will complete the activation process - once your software is activated you may delete the Request.txt and the Request_code.txt files

Separate documents provide Network Installation Directions:

• Spartan'10 click here to open Spartan'10 Network Installation Directions (pdf file)
• Older Spartan licenses: click here to open Network Installation Directions (pdf file)

The standard single license of Spartan is managed via a HASP (USB key) and allows for the software to be installed on multiple machines and accessed by whichever machine has the USB key plugged in. Insert the Spartan CDROM into your CD drive, installation should begin automatically, if not:

• Open My Computer
• Open the disc image in your CD drive
• Double click on the Setup icon
• You must agree to the license agreement to continue installation
• If prompted to choose a licensing option, select 'Hardware Key' for HASP (USB key) installation - this will include the drivers necessary for your computer to recognize the USB HASP in the installation procedure
• Follow the prompts provide by the installation wizard to complete installation.

In Windows versions of Spartan, file import is managed via the File Menu - Open option. Select 'All Files' from the drop down menu. The current Spartan'06 for Windows version recognizes several molecule file types, including:

• Standard Spartan file formats (.spartan, .spinput, .spentry) and Odyssey files (.odydata)
• Published .smiles (1-D) files
• SKC, TGF, and SD/SDF (2-D) files (MDL file formats)
• CDX (2-D) file (CambridgeSoft file format)
• Additionally, 3-D file import is available for MacroModel, Sybyl Mol and Mol2, PDB, CIF, and XYZ files

In the Windows versions of Spartan, file export is managed via the File Menu - Save As option. Click on the 'Save As Type' drop down menu to specify file type. In addition to a number of Spartan files, export is available for the following file types*:

• SMILES
• SKC
• TGF
• SDF
• MacroModel
• SYBYL Mol
• SYBYL Mol2
• PDB
• XYZ
• Image export is available via: JPG, PNG, BMP files
• Animation export is available via AVI files

*NOTE saving files in non-native Spartan file types may result in a loss of data.

Spartan can be seamlessly hyperlinked into PowerPoint, either by:

• Hyperlinking Individual Models (.spartan files)

• Hyperlinking Spartan directly

See the following items for the corresponding instructions.

General Note: When you run PowerPoint and use Spartan hyperlinks, be sure to close Spartan before moving back to PowerPoint (or you will end up with multiple sessions of Spartan running).

• Save the model that you want to hyperlink as a .spartan file in a folder of your choice.
• Before you can hyperlink the file into your PowerPoint presentation, you must "register" the .spartan file extension with the Windows operating system (only this way PowerPoint will know that it needs to start Spartan on encountering your hyperlink):
  1. Try to directly open the .spartan file by double clicking on its icon. If Spartan starts up and the model displays, you don't need to do anything else. Move on to item 3).
  2. If Spartan doesn't start up, right-click on the .spartan file and select Open With. In the resulting dialog, navigate to the Spartan folder and select "Spartan.exe" (name will vary depending on Spartan version). In most cases, you will find the Spartan folder in the "Program Files - Wavefunction" folder in "Local Disk (C:)".
  3. Check the "Always Open With This Program" option (this creates a registry entry).
  4. Open the file, then close Spartan.
• Any file of the type .spartan can now be hyperlinked into PowerPoint slides, either via the "Action Settings" attribute or via the "Hyperlink" attribute. All features of the Spartan interface (build, measure, display surfaces, etc.) are fully available.
• See the FAQ "How do I suppress the security dialog when hyperlinking into PowerPoint?" if you want to avoid the standard "security dialog" when opening hyperlinked .spartan files.

If you link directly to Spartan, you can access any .spartan file, or build your own model (just as opening the program).

• In your PowerPoint slide, select the object that you wish to hyperlink.
• Right-click and select Action Settings.
• Select Run Program and browse for either "Spartan.exe" (name will vary depending on which Spartan version you have)

Clicking on the object in the PowerPoint slide (when in presentation mode) will now take you to the Spartan program. From here, you can open any .spartan file or utilize any Spartan feature.

Yes, to export data from the Spartan spreadsheet to Excel (or other formatted cell programs), you can use the conventional Copy and Paste approach.

Use the left mouse button to highlight, hold the button down while dragging the mouse to select multiple cells.

Choose either Edit Menu - Copy or right click and select Copy, or use the CTRL+C keys to copy.

Open Excel and use either the Edit Menu - Paste or CTRL+V keys to paste the copied Spartan data.

There are several ways to create a multi-molecule list in Spartan:

• Building. Build an initial molecule and then select 'File Menu - New Molecule' (NOT File Menu - New) and build a second molecule. To continue adding molecules to the list, simply select the 'New Molecule' entry in the File menu before building the next molecule. Once you've completed the list, you may scroll through the molecules by using the step forward/backward keys in the lower left corner of the viewer window, or by selecting (clicking on) the molecule you wish to view from within the Spartan spreadsheet (Display Menu - Spreadsheet)
• Appending. Once saved, a molecule (or a list of molecules) maybe appended to a new molecule. Build an initial molecule, then select 'File Menu - Append Molecule(s)'. Use the browser to locate the .spartan file you wish to append to your current document. In this way, a list file can be constructed from previously saved Spartan documents (files).
• Database Retrieval. Molecules retrieved from the Spartan Molecular Database or the Cambridge Structural Database can either be retrieved to a New File or the Current File, when retrieving a database entry to the current file, or when retrieving multiple database entries to either the current file or to a new file -- a multi-molecule list is created.
• Calculations. Certain calculations will also result in the creation of a multi-molecule list. Energy Profile, Conformer Distribution, or Transition State Geometry (with IRC selected) will result in the creation of a new list file at the completion of the calculation. The last line in the Output (Display Menu - Output) will provide the location of the new list file.
• Make List. If an IR calculation has been performed, the user can create a list file representing the molecular vibration of any of the calculated frequencies by selecting (clicking on) a frequency in the Spectra dialogue (Display Menu - Spectra) and then selecting (clicking on) the Make List button.

Any list file (see above) can be exported as an animation via the Fie Menu - Save As option and selection of AVI as the file type. AVI files can be viewed and edited with most media players.

The default colors in Spartan can be modified by using the Set Color dialogue (choose Colors from the Options menu) items are selected by clicking and color changes are available for:

• Spartan atom colors
• Bond colors (default is gray)
• Plot colors (selected by clicking on a plot axis or on a plotted curve)
• Background color
• Hydrogen Bond color
• Constraint indicator color
• NOE constraint indicator color
• Substituent Attachment Indicator color
• Ribbon colors

A special case involves changing the color of Spartan's labels, in order to do this, you must hold down the SHIFT key when selecting Colors from the Options Menu.

Spartan provides visualization of .pdb (Protein Data Bank) files, or of polypeptides and polynucleotides constructed from within Spartan with the option of visualizing the secondary structure using the popular 'Ribbon' style. This is turned on/off via a 'toggle' selection of Ribbons from the Model Menu. Additional configuration options are available by selecting Configure from the Model Menu and selecting the Ribbon tab in the resulting dialogue :

• Color as monochrome
• Color by Secondary Structure
• Color by Strand
• Color by Residue

'Style' choices include:

• Ribbons (default)
• Lines
• Beads

To display hydrogen bonds as dotted lines select (click on) Hydrogen Bonds in the Model Menu.

Note: Spartan provides visualization of hydrogen bonds representing non-bonded interactions between a nitrogen, oxygen, or fluorine atom and a hydrogen attached to either nitrogen, oxygen, or fluorine. where hydrogen bonding distances range between 1.6 and 2.1 Angstroms and the X-H-Y bond angle (where X & Y = N, O, or F) is greater than 120°.

To query the numerical values of any bonded or non-bonded distance, angle or dihedral (torsion) angle, choose from the Geometry Menu:

• Measure Distance - Select (by clicking) either a bond or two atoms to measure distances, distance appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the distance
• Measure Angle - Select (by clicking) either two bonds or three atoms to measure an angle (note the selection order matters), the angle value appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the angle
• Measure Dihedral - Select (by clicking) either three bonds or four atoms to measure a dihedral (torsion angle), the selection order matters, the dihedral angle value appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the dihedral angle

Note: Queries may also be made between user defined points or planes.

Molecules in Spartan may be labeled by selecting Labels from the Model Menu. By default the Spartan label which identifies atoms is displayed. Labels can be customized by selecting Configure from the Model Menu and selecting the Labels tab:

• Label (Spartan label)
• Element
• Mass Number
• R/S Chirality
• Mulliken Charge
• Electrostatic Charge
• Natural Charge
• Exposed Area
• NMR Chemical Shift

Note: Users can customize the default Spartan atom labels when in View mode by selecting Display Menu - Properties and then selecting an atom, the resulting Atom Properties dialogue contains a label field which is user-accessible. Enter in your desired label and press the ENTER key on your keyboard.

Yes. Select Fonts from the Options Menu and Font type, style, and size are available for user specification.

Note: Zooming In (SHIFT key + Right Mouse button) increases both the size of the model and the label.

With a plot displayed and when in the View mode choose Properties from the Display Menu and click on either the plot or the Y axis to select it. This will display the Plot Properties or Curve Properties dialogue, respectively:

• Select the Scale Tab
• Locate the Label Size Field
• Use the Up (or down) arrows to adjust the label size

The Minimize Energy button/icon is used to reduce the strain energy of a molecule during the building process and typically upon completing the construction of a molecule. This button is a shortcut to performing an Equilibrium Geometry calculation using the MMFF (Merck Molecular Mechanics Force Field) and attempts to:

• Minimize distortion from parameterized "ideal" bond distances and angles
• Optimize geometry with respect to non-bonded van der Waals interactions
• Optimize geometry with respect to Coulombic interactions

Note: MMFF94 was parameterized for common organic molecules, the Minimize Energy function produces a local energy minima for organic molecules, but may produce undesirable results for molecules with metal atoms.

In the Add Fragment [+] mode, inversion of a chiral center is achieved by holding down the CTRL key and Double Clicking (left mouse button) on the chiral atom. It is useful to have R/S chirality selected as a Label to confirm you have inverted as you wanted. In some heterocyclic rings it may be impossible to invert chirality in this manner. If this is the it may be necessary to physically 'break' a bond, invert chirality, then re -'make' the bond in order to invert a chiral center.

To invert absolute configuration (select the alternate enantiomer), in the Add Fragment [+] mode, hold down the CTRL key and Double Click (left mouse button) anywhere on the molecule. (If you happen to double click on a chiral center, you may end up inverting on this center.)

Spartan uses Open GL to render display of molecules in 3D and enable 3D building. Sometimes, installing new software (or downloading updates) can result in an over-write of Open GL drivers for your system's graphics card. Spartan requires a complete set of OpenGL graphics drivers in order to function properly. If you notice calculated surfaces (molecular orbitals, electron densities, electrostatic potentials, etc.) are not displayed properly, or if you are unable do build by adding a fragment to an open (yellow) valence -- it is likely that you need to update your Open GL drivers.

First identify what graphics card you have:

Right Click on your desktop
Click on Properties
Choose Settings Tab
Click on Advanced Button
Choose Adapter Tab

Visit your graphics card manufacturer's web site and locate the downloads section. . .

Click here for NVIDIA downloads
Click here for ATI downloads

Download the latest drivers for your graphics card and operating system. This will typically address any Open GL problems.