ODYSSEY
Frequently Asked Questions
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General With what types of classes can ODYSSEY be used?

ODYSSEY is widely used in first-year college courses as well as high school science classes. Since diverse content is included with the program, regular chemistry students as well as honors and AP/IB students will find suitable material. Many middle and high school Physical Science teachers have also benefitted from using ODYSSEY's powerful visualization technology with their classes.

General Does the program replace conventional textbooks?

ODYSSEY provides instructors with a powerful tool to introduce and enforce many of the molecular concepts of chemistry. For the most part, this is accomplished through visualization exercises and laboratory-style experiments. Effectively, ODYSSEY does not replace, but complement textbooks. The program also complements other teaching software where the emphasis is more on repetitive problem drills.

General What is the difference between ODYSSEY and molecular visualizers?

Molecular visualizers such as "Jmol," "Chime," and "Rasmol" are quite popular. The functionality of these visualizers is a small subset of that of ODYSSEY and essentially amounts to two core features:

Unlike molecular visualizers, ODYSSEY is a full-fledged simulation and teaching tool. Unique features include the following:

General How is the program different from Flash-based simulation software?

ODYSSEY as well as many Flash animations and Java applets purport to employ a "simulation" approach. However, despite the same label, the two types of software have little in common:

Versions Is ODYSSEY available in different versions?

The program is available in two versions:

The college version (which in terms of "size" is about 50% larger than the high school version) is also appropriate for Advanced Placement.

Similar to introductory textbooks, both versions are available as Student Editions as well as annotated Instructor's Editions. While the functionality of the Student Editions is a subset of that of the Instructor's Editions, it is still comprehensive and allows for ODYSSEY's entire spectrum of scientific simulations and build operations. The Student Edition, however, does not include the Answer Key for the worksheets.

Versions Under what operating systems will ODYSSEY run?

ODYSSEY is available for Windows (either Windows 7, Vista, or XP) and Mac OS X (either 10.7 Lion, 10.6 Snow Leopard, or 10.5 Leopard).

Versions Will ODYSSEY work on a 64-bit computer?

Yes, ODYSSEY can be run with either 32-bit or 64-bit operating systems.

Versions Is ODYSSEY available for Linux?

No, ODYSSEY is not available for Linux.

Versions Is ODYSSEY offered for languages other than English?

ODYSSEY is available in English for Windows and Mac OS X. Different versions of the software are also available in Spanish (Windows only) and Japanese (Windows and Mac OS X).

Requirements Will the program run under any Windows operating system?

ODYSSEY requires Windows 7, Vista, or XP. The program will not run under older operating systems, such as Windows 98 or Windows ME.

Requirements Will the program run on any Macintosh?

ODYSSEY requires Mac OS X 10.7 (Lion), 10.6 (Snow Leopard), or 10.5 (Leopard). The program is not compatible with earlier releases of OS X.

Only Intel-based chips are supported.

Requirements Does ODYSSEY require an expensive computer to run on?

No, ODYSSEY will successfully run on essentially any modern laptop or desktop computer (excluding "netbooks"—they are exceedingly slow in terms of speed and using the program with a small size screen is cumbersome). This includes any computer with a Core Duo-type chip (or the equivalent from AMD). For older computers, the minimum requirement is a clock speed of ~2 GHz (Pentium 4 / Celeron) or ~1 GHz (Pentium M and various AMD chips).

Requirements Will ODYSSEY run on machines below the minimum requirements, albeit a little bit more slowly?

On computers that don't meet the minimum requirements, ODYSSEY will run so slowly that dynamic simulations are basically not feasible. Since such simulations are central to the program, ODYSSEY will effectively not be functional.

Requirements Does the program require online connectivity?

ODYSSEY is a locally running application that does not access the Internet if you use it with the included content. The only exception is the activation step if you purchase the program with an activation code: In that case, the program briefly accesses the Internet while installing.

Requirements Does ODYSSEY run on tablet PC's?

Yes, ODYSSEY runs on Windows tablet computers (provided the operating system is either Windows 7, Windows Vista, or Windows XP).

Requirements Does ODYSSEY run on the iPad?

No, ODYSSEY is not available for the Apple iPad.

Requirements Can the Windows version be run on a Macintosh that has Boot Camp and Windows installed?

Yes, ODYSSEY can be run in the Windows mode of a Boot Camp-configured Macintosh without any loss of performance. Note that you need valid and independent licenses both for ODYSSEY and the operating system (Windows 7, Vista, or XP).

Requirements Can the Windows version be run under Mac OS X using Parallels?

While it is possible to run the Windows version of ODYSSEY on a Macintosh using Parallels, this is not recommended because of a significant degradation in performance.

Requirements Doesn't the fact that the program uses a web browser mean that it is an online application?

If used with the included content, ODYSSEY is a locally running application that does not access the Internet. In other words, Internet Explorer/Safari is used as local content browser rather than a "web" browser.

The only exception is the activation step if you purchase the program with an activation code: The program accesses the Internet just once (namely on installation) in order to activate the program.

Requirements What are the graphics card requirements?

There are no specific requirements. On Windows machines, you can use the Reduced Graphics for Slower Machines option in Tools Preferences if the graphics performance seems unsatisfactory.

Requirements Can the program be run in 8 bit color mode?

No, ODYSSEY does not support 8 bit color mode ( = 256 Colors).

Installation How do I install the Windows version using an activation code?

The following steps require that you are connected to the Internet and that your Firewall is not so superstrong that it interferes with basically any communication with the outside world:

Installation What do I do if I purchased ODYSSEY with an activation code and my online activation attempts are failing?

Use the offline activation procedure. See FAQ "How do I install using an activation code if I don't have Internet access?"

Installation How do I install using an activation code if I don't have Internet access?

If you purchased ODYSSEY with an activation code and your computer does not have Internet access (or if you have a particularly strong Firewall that foiled your activation attempts), you need to activate offline. The following steps describe the required steps for Windows—the procedure for the Macintosh is analogous:

Installation How do I install using an individual USB key?

The USB key version of ODYSSEY allows for the software to be installed on multiple machines; it can then be accessed wherever the USB key is plugged in (note that simultaneous use on multiple machines requires a USB network license instead). The following steps describe the required steps for Windows—the procedure for the Macintosh is analogous:

Installation How do I install using a Network License?

The following document provides network installation directions:

Installation What do I do if the Windows program crashes immediately after installation?

Try to lower the "Graphics Hardware Acceleration" if ODYSSEY crashes immediately after installation:

Installation How do I uninstall the Windows version?

To uninstall the Windows version of ODYSSEY:

If the Uninstall shortcut in the ODYSSEY program group is not available:

User Interface Can I change the size of the text, properties, and plot areas?

The user can control the screen layout by changing the size of the window tiles:

Vertical separators (between Build/Cell/Plots area, Sample area, and Text area):

Horizontal separator (between Sample area and Properties area):

User Interface How do I change the size of the text?

The text size can be altered independent of the screen resolution.

ODYSSEY will remember the new setting the next time you start the program.

User Interface Can I change the fonts?

The fonts of the main text panel as well as of other text strings in the program cannot be changed.

User Interface Can I use an icon toolbar similar to the one seen in SPARTAN?

To display a toolbar with icons for various types of Select, the essential Build modes, and operations such as Minimize, Evaluate, and Name:

User Interface Does clicking on the Refresh/Reload icon only affect the currently displayed sample or page?

No, while clicking on the refresh icon takes you back to the subpage that you were on, it refreshes all samples and all subpages of the current experiment. (Experiments in other tabs are unaffected by a refresh.)

A Reload option is also available in the shortcut (right-click) menu when the cursor is within the text area. Unlike the general reload, the effect of this particular reload is limited: It only refreshes the HTML of the current subpage, i.e., it does not refresh the molecular sample and it does not refresh other subpages.

User Interface Can I suppress the text panels of open pages?

In the Instructor's Edition, the text panel can be temporarily hidden (the toolbar must be displayed):

User Interface Can I put the program into true Full Screen Mode, similar to PowerPoint?

ODYSSEY can be put into presentation-style full screen mode:

To exit full screen mode:
User Interface What do the colors in the Periodic Table stand for?

The Periodic Table (in the Tools menu) can be displayed with the following color overlays:

User Interface Where do I declare the charge when I build an ion with the Electronic Model Kit?

Click on Set Charges... in either the Entry-Level or Advanced builder, then use the up/down arrows to set the charge (labeled "molecular" charge for the sake of generality). In build mode, the charge is displayed for all charged species.

Plotting and Printing How do I avoid that datapoints are covered up by a plot's caption?

To move the caption of plots (e.g., in order to expose datapoints "hidden" behind the caption):

Plotting and Printing How do I print snapshots of molecular samples?
Plotting and Printing How do I print a plot?
Plotting and Printing How do I print the text panel?
Plotting and Printing How do I print the properties table?

Use the computer's screen-capture facility (many machines have a special "Print Screen" key):

Plotting and Printing How do I print the entire screen?
Plotting and Printing How can I suppress the Windows "Blocked Content" message bar when printing PDF-formatted worksheets?
Classroom Use Can ODYSSEY be used with interactive whiteboards?

Yes, ODYSSEY is well suited for classrooms that are equipped with Smartboards or other interactive whiteboards.

Classroom Use Can I use the program with PowerPoint?

ODYSSEY can be seamlessly hyperlinked into PowerPoint. You have the choice among the following possibilities:

In each case all features of the ODYSSEY interface (simulation control icons, etc.) are fully available after following the hyperlink in your PowerPoint presentation. See the following items for detailed instructions on how to create hyperlinks.

Classroom Use How do I hyperlink an individual molecular sample?
Classroom Use How do I hyperlink the program's initial page?

If you link to ODYSSEY's initial page, you can access any experiment and/or sample via that hyperlink:

Clicking on the object in the PowerPoint slide (when in presentation mode) will now always take you to the initial page of ODYSSEY. You can go wherever you wish from there.

Classroom Use How do I hyperlink an experiment or a stockroom page?

ODYSSEY experiments and stockroom pages can be hyperlinked into PowerPoint presentations. Note that the hyperlink must refer to a .odyssey in its original location in the ODYSSEY folder—a copy of the file somewhere else will not do.

Classroom Use How do I suppress the Windows security dialog when hyperlinking into PowerPoint?

To suppress the "Security Dialog" when hyperlinking into PowerPoint (all of the actions are required):

Classroom Use How do I incorporate animations (sequences of frames) into my classwork?

To incorporate ODYSSEY animations (dynamic sequences of frames) into lectures, PowerPoint presentations, laboratory experiments, and homework assignments:

Since ODYSSEY is organized around the paradigm of live, interactive simulations, corresponding "movies" cannot be saved. (Please note that the license agreement explicitly prohibits capturing of dynamic ODYSSEY simulations by any means.)

Classroom Use Are my students prevented from building "nonsense" molecules?

No, just as is the case for plastic model kits, students are not prevented from building chemical nonsense structures. However, the "Validity" function provides feedback regarding the chemical reasonableness of any user-built or pre-built structure:

Working with this functionality allows students to assimilate chemical rules in an open-ended, highly interactive manner. Note that this approach is distinctly different from that of typical "drilling software" where the chemical intelligence has been programmed into a sequence of dialogs that leave the student with essentially nothing but the memorization of rules.

Classroom Use How can I assess student work carried out with ODYSSEY?

ODYSSEY includes questions with many of the molecular labs. Assessment can be carried out in several ways:

Molecular Visualization How do I Animate a Sample Whose Dynamics Button is Faded Out?

Some of the samples in ODYSSEY are "static", i.e., the toggle below the sample for initiating a room temperature simulation is faded out. Samples are shown in this manner for one of the following reasons:

If desired, even static samples can easily be animated:

Molecular Visualization Can I depict lone pairs?

To display a schematic representation of lone pairs (where applicable):

Note: For samples with "electronic surfaces," the visualization of lone pairs may not always be available.

Molecular Visualization Why can't I highlight the collisions of the sample of gas that I built?

The "Collisions" attribute (in the Style menu) is only available for samples whose density is not too high (this protects the computer from being overwhelmed by collision counting in higher density samples). A rule of thumb is that letting the pressure drop to less than ~10 atm (use Build Cell Gas) will make the "Collisions" attribute available.

Molecular Visualization Can I highlight the sequence of residues in proteins and nucleic acids?

Proteins and nucleic acids that contain explicit residue information (this includes samples that have been built with ODYSSEY's Peptide or Nucleotide builder as well as PDB files from the Protein Data Bank) can be displayed as "Ribbon" models with a visual indicator for the sequence of residues:

Molecular Visualization Why do molecules of liquids and solids sometimes "disappear"?

In simulations of liquids or solids, you may notice that some molecules or atoms seem to leave the simulation cell, i.e., when close to one of the boundaries they often seem to be gone a few moments later. If you look carefully, however, you will also notice the opposite, namely "new" molecules (or atoms) that seem to enter the simulation cell.

What is going on? The explanation is that there really aren't any "boundaries" when ODYSSEY simulates a liquid or solid—despite the obvious presence of a simulation cell. What the program really uses is called Periodic Boundary Conditions: essentially, the simulation cell "wraps around" in each of the three dimensions. If, for example, a molecule leaves the simulation cell towards the right, the same molecule re-enters from the left! In effect, we have allowed the molecule to cross the system boundary while not losing anything—the system density remains perfectly constant.

The huge advantage of this approach is that there are no walls in the system that can interfere with the calculated bulk properties.

Molecular Visualization Why do some molecules at the simulation cell boundaries look "clipped"?

ODYSSEY generally employs "Periodic Boundary Conditions" when simulating liquids and solids (see FAQ "Why do molecules of liquids and solids sometimes disappear?"). By default, the visualization is such that molecules always leave and re-enter the simulation cell as “complete” entities, i.e., all atoms of a given molecule are drawn either on one side or on other side of the simulation cell.

Alternatively, a visualization mode is available where any molecules that fall right on the boundaries are shown with some of their atoms still on one side, while the molecule's other atoms are already shown re-entering on the other side. This will make all surfaces of the simulation cell look “smooth” (not corrugated). At the same time, it will also make some molecules look “clipped”, i.e., some atoms seem to be missing (in fact, they can be seen on the other side of the simulation cell). To select this type of visualization:

Note that the clipping preference only affects the visualization of molecular systems—the underlying simulations are completely unaffected by the preference setting. Also note that some systems (such as liquid sulfur) have a fixed setting for the periodic boundary clipping that is not overridden by the preference setting.

Molecular Visualization Can I show two samples at the same time?

Yes, use the View Side-by-Side function (or the Compare icon in the toolbar) to add a second sample to the one originally shown.

Molecular Visualization What can I do if the graphics performance is poor, particularly when using the "Space Filling" style?

On Windows computers, you can try the following:

Molecular Visualization What can I do about unsatisfactory graphics performance when running on battery?

On Windows computers, you can try the following:

Physical Properties How do I measure physical properties?

To query the numerical values of physical properties:

Physical Properties How do I change the physical units?

To change the default settings:

Physical Properties Can I overwrite the "slider" limits in the property table?

Built-in limits for temperature, volume, and composition sliders can be overwritten by entering the property value as a numerical value:

Note: The limits of the corresponding slider are immediately updated to include the newly requested value.

Physical Properties How do I minimize the energy of a sample?

To minimize the energy of a sample:

Note: Systems with a container boundary (typically gases) or under periodic boundary conditions (liquids and solids) are minimized at constant volume.

For some samples, particularly those with electronic (wavefunction-based) data, the energy minimizer and the dynamics option are deliberately disabled. If you really must minimize the energy of such a system, you can still do so after saving the sample as a new file.

Physical Properties How are the energies calculated?

For each molecular sample, ODYSSEY calculates the energy of interaction between the atoms that are present, regardless of whether the sample is an isolated molecule or a bulk phase with many molecules. The "potential function" is very complicated—there are many hundreds of parameters for all the elements and valence states encountered in chemical compounds. At least conceptually, however, the potential function can be thought of containing the following main terms:

There are a few other terms, but essentially it is the sum of these energies that yields the total energy of a given system. Calculation of the derivatives of the total energy with respect to the coordinates of all the atoms yields the intermolecular forces that are at the heart of the algorithm that takes the system from one time step to the next. As the energy depends on the coordinates of all the atoms in the system, the calculation has to be repeated even if only a single atom moves.

Physical Properties How are enthalpies calculated?

In order to allow for an intuitive interpretation of the thermodynamic consequences of temperature and phase changes, ODYSSEY adopts a unique reference state for enthalpies. The displayed values (from empirical formulas that represent best fits of experimental data) are always relative to the elements in their standard states at 25°C. Note that this is different from what is implicit in many thermodynamic tables:

ODYSSEY abstains from working with varying reference states.

Physical Properties How are entropies calculated?

ODYSSEY displays standard entropies. The algorithm used depends on the complexity of the given system and involves certain combinations of analytical statistical thermodynamical theory and empirical formulas (with the latter representing best fits of experimental data).

Physical Properties How are free energies calculated?

In order to allow for an intuitive interpretation of the thermodynamic consequences of temperature and phase changes, ODYSSEY adopts a unique reference state for free energies. The displayed values (calculated from the underlying enthalpy and entropy data) are always relative to the elements in their standard states at 25°C. Note that this is different from what is implicit in many thermodynamic tables:

ODYSSEY abstains from working with varying reference states.

Physical Properties How are hydrogen bonds identified?

ODYSSEY identifies a hydrogen bond if an atom with an attached hydrogen is close to another atom and all of the following criteria are satisfied:

Physical Properties Do the calculated properties reproduce experimental data?

There is no blanket answer to the question. In many cases, there is qualitative agreement between calculated and experimentally measured properties. Particularly "trends" (such as variation with atomic mass, variation with dipole moment, or variation with temperature) are very often predicted correctly. Predictions that are quantitatively correct are rare as the program employs models that are computationally inexpensive and therefore imperfect.

While not very common, outright failures also occur. However, it should be kept in mind that the presence of failures and limitations is a defining characteristic of all models—not only scientific models, but also models anywhere else. The pedagogical value of models derives from their ability to be experimented with, not from being perfect replacements of the "real thing."

Physical Behavior Why do the vapor molecules of a given substance don't seem to move much faster than the liquid molecules?

In order to facilitate observations of a wide variety of systems, ODYSSEY autoscales the size of the simulation cell to the screen size regardless of the physical state of the substance. As gas phase simulation cells are typically much bigger than condensed phase simulation cells (see the Cell Dimensions displayed above the sample area!), the net motion in the gas phase is in fact much faster than the net motion in the liquid phase.

In accordance with temperature, the molecular speeds themselves are also higher in the gas phase than in the liquid phase:

Physical Behavior Does ODYSSEY assume ideal gas behavior?

No, ODYSSEY never assumes ideal gas behavior. Gas molecules are always modeled as particles of finite volume that exhibit non-negligible interactions (if sufficiently close).

Nevertheless, ideal gas behavior will be observed in many situations, namely whenever the physical conditions happen to closely correspond to the assumptions that are implicit in the Ideal Gas Law.

Physical Behavior Can I simulate the liquid-vapor transition?

The liquid-vapor transition can easily be simulated for most liquids:

Physical Behavior Will gases condense on cooling?

Yes, given sufficient simulation time and a sufficiently low temperature, samples of gas will eventually show condensation. However, the condensation will happen via the formation of irregular molecular clusters rather than through the formation of a "neat" horizontal interface. The reason for this is the insignificance of gravitational forces in samples that are as small as those simulated by ODYSSEY (see FAQ "When I turn a partially filled simulation cell "upside down," why doesn't the liquid flow to the bottom?").

Physical Behavior When I turn a partially filled simulation cell "upside down," why doesn't the liquid flow to the bottom ?

The reason for this at first glance strange behavior is that gravitational forces are so weak that they do not make a difference on the time scale of molecular simulations. Phenomena that crucially depend on the effects of gravity, such as the flow of liquids and the formation of "neat" interfaces, are therefore not reproduced by the simulations. There is simply not enough time for these phenomena to become noticeable.

Effectively, the behavior observed in ODYSSEY simulations is the same as that seen for real-world, macroscopic samples in the absence of gravity (such as on any orbiting spacecraft).

Physical Behavior If I cool a liquid to below its freezing point, why doesn't it freeze?

ODYSSEY focuses on real simulations of physical phenomena, rather than on cartoon-style animations. While the freezing transition can be simulated, it is very hard to do and requires sample sizes and time scales that lie beyond the scope of ODYSSEY.

Physical Behavior If I melt a crystal of ice, why doesn't its density increase?

For a number of reasons, ODYSSEY performs its simulations with unit cells of constant volume. The user has to manually adjust the volume in order to represent changes in density:

Alternatively, the Build Cell Liquid tab can be used for density adjustments.

Physical Behavior When I dissolve a molecule of hydrogen chloride in liquid water, why doesn't it dissociate?

While ODYSSEY is capable of representing a large variety of physical and chemical processes, the program cannot directly carry out real-time simulations when one or both of the following apply:

The dissociation of strong acids falls into the first one of these categories. If desired, models of the dissociated species—such as (Cl–)aq and (H3O+)aq, (H5O2+)aq, or (H7O3+)aq—can be built with ODYSSEY's Electronic Model Kit.

Physical Behavior If I have a sodium chloride–water interface, why don't the ions gradually dissolve?

While ODYSSEY is capable of representing a large variety of physical and chemical processes, the program cannot directly carry out real-time simulations when one or both of the following apply:

The process of dissolving an ionic solid falls into the second one of these categories. The issue can still be addressed by building "snapshots" of the system in various stages of the dissolution process. (There is an entire Molecular Lab dedicated to this topic.)

Physical Behavior I built the same system as found in the Molecular Stockroom, but it doesn't behave the same. Why?

When building molecules and bulk phase samples from scratch, ODYSSEY draws on a set of all-purpose rules and parameters (since the structure space of chemistry is huge and the computer obviously doesn't exactly know what you are after). Models in the Molecular Stockroom, on the other hand, are sometimes defined with custom settings that help with improving the general quality of the model.

As a consequence, self-built models will occasionally not "behave as well" as the pre-built models. However, it is rare for a self-built model to behave completely differently.

Importing / Exporting / Annotating Can all molecular samples be saved?

Yes, the currently displayed sample can almost always be saved as an .xodydata file into locations outside of the ODYSSEY folder (the ODYSSEY folder is Read Only in order to preserve the integrity of the software):

The following restriction applies when saving samples:

Importing / Exporting / Annotating In what format should three-dimensional samples be saved?

The default file format is ".xodydata" which is XML-based and includes a complete record of the model except for wavefunction-based surfaces (the latter can be read by ODYSSEY, but not be saved).

The alternate .spinput format is needed for exporting files to Wavefunction's program SPARTAN.

In the Instructor's version of the program, you can also make yourself an "Expert" (go to the Preferences dialog). You are then able to save samples as SMILES strings—these are understood by many other chemistry programs.

Importing / Exporting / Annotating Can I open saved samples with "drag and drop"?

All ODYSSEY files (.xodydata or .odyssey) and also all .spartan files can be opened by dragging the file onto the desktop shortcut created by the installer.

Importing / Exporting / Annotating Can pictures of the molecular samples be saved?

Yes, screen shots of molecular samples can be saved in several formats:

Tip: For best resolution, zoom in prior to saving the screenshot. In the Instructor's Edition, you can furthermore hide the text panel using the corresponding toolbar icon.

The clipboard (Edit Copy) can also be used to export pictures.

Importing / Exporting / Annotating Can I import files from other modeling programs?

ODYSSEY reads .pdb files (generated by most other modeling programs and also the file format of many databases), .spartan files (generated by Wavefunction's program SPARTAN), and SMILES files (.smi). Other file formats understood include XYZ (.xyz), ChemDraw (.cdx), and ISIS/Draw (.skc).

Use File Open in order to import an external file.

Importing / Exporting / Annotating Is ODYSSEY compatible with Protein Data Bank files?

Yes, ODYSSEY can serve as a high quality viewer for any Protein Data Bank file.

Importing / Exporting / Annotating Can I annotate the text pages?

Yes, all ODYSSEY pages can be annotated:

The annotations for a given Experiment or Stockroom entry are retained by the computer and will be shown whenever you return to the corresponding Notes page later.

Importing / Exporting / Annotating Can I add my own content?

Yes, in the Instructor's Edition of the program, all molecular labs are editable. Entirely new labs can also be created using a template.

If uploaded to the instructor's own website, the custom content can be made accessible to students by providing hyperlinks (ODYSSEY will automatically open when clicking on a corresponding hyperlink in a webpage).

Please contact Wavefunction with suggestions for incorporation of new content into future releases of the program!