Frequently Asked Questions
Internet Explorer Users: To view this file, you
must allow "active content" to run in your web browser.
- To give one-time permission: Right-click on the yellowish security toolbar above and select Allow Blocked Content...
- To change your security settings permanently: Enable Tools ® Internet Options ® Advanced ® Allow active content to run in files on My Computer, then reload this page.
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 school teachers, high school Physical Science teachers, etc. 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:
-
Archived models of small molecules as well as biomolecules
can be visualized in three dimensions.
-
The appearence (style) of the models can be changed.
Unlike molecular visualizers, ODYSSEY
is a full-fledged simulation and teaching tool. Unique features include the following:
-
An open-ended model kit allows students and teachers to build almost any chemical structure imaginable.
-
Bulk phase systems (solids, liquids, and gases) are treated on an equal footing with individual molecules.
-
Molecular motion can be studied with real-time, open-ended simulations.
-
Physical manipulations can be carried out that truly change the nature of a given system.
-
Systems of a huge diversity can be studied (literally from hydrogen to DNA and from liquid water to complex crystals).
-
Rich teaching content is directly integrated into the program.
-
The quality of the three-dimensional visualization is unparalleled in a teaching tool.
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:
-
The models used by ODYSSEY
are always fully three-dimensional. More often than not, the models of Flash-based simulations
are either two-dimensional or do not represent any molecular entities at all.
-
By and large, ODYSSEY
uses models that are "realistic" representations of
molecular matter. The models of Flash-based simulations
are almost always highly abstract and cartoonish.
-
ODYSSEY is an open-ended, general purpose tool
that can be used for many types of queries. Flash-based simulations
are highly focused on a single message at a time.
-
Using ODYSSEY for instruction has all the hallmarks
of a computer-based laboratory. Flash-based simulations provide a "viewing" experience
similar to that of mediaplayers.
-
Like a giant microscope, ODYSSEY provides a computer-based look at the
molecular world. Flash-based simulations are essentially animated analogs of
textbook illustrations.
Versions
Is ODYSSEY available in different versions?
Similar to introductory textbooks, ODYSSEY is available as a Student Edition as well
as an annotated Instructor's Edition. The functionality of the Student Edition is a comprehensive
subset of that of the Instructor's Edition. The Student Edition does not include the Answer Key for
the more than 40 worksheets.
Versions
Under what operating systems will ODYSSEY run?
ODYSSEY is available for Windows and the Mac OS X operating system.
The installers for the two platforms are on the same disk, but there
are two separate disks for the Student and Instructor's Editions.
Versions
Is ODYSSEY available for Linux?
No, ODYSSEY is not available for Linux.
Versions
Is ODYSSEY offered for languages other than English?
ODYSSEY is currently available in English (Windows/Macintosh), Spanish (Windows only), and Japanese (Windows/Macintosh).
Requirements
Will the program run under any Windows operating system?
ODYSSEY requires Windows Vista, Windows XP, or Windows 2000.
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 10.4.6 Tiger.
Both the new generation of Intel chips and the older generation of PowerPC chips are supported.
However, the program will not run under older releases of the
Macintosh operating system.
Requirements
Does ODYSSEY require an expensive computer to run on?
No, ODYSSEY will successfully run on essentially any
computer that has been purchased within the last ~3 years. The minimum requirement is
a clock speed of ~2 GHz (Pentium 4 / Celeron, both running under Windows) or ~1 GHz (Pentium M / Core Duo / various AMD chips, all running under Windows; Core Duo / PowerPC, both running under MacOS X).
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 not be functional.
Requirements
Does the program require online connectivity?
No, ODYSSEY is a locally running application that does not access
the Internet.
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 the program run on tablet PC's?
Yes, ODYSSEY
runs on Windows tablet computers (release 1.3 and up).
Requirements
Can the Windows version be run on a Macintosh that has Boot Camp and Windows XP 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 the operating system (Windows XP)
and ODYSSEY.
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
Can the Windows version be run on a Macintosh using Virtual PC?
No, ODYSSEY cannot be run on a Macintosh computer
using Virtual PC.
Requirements
I use an alternate browser, such as Firefox.
Is Internet Explorer still required for the Windows version?
Yes, ODYSSEY's Windows version requires that Internet Explorer (version 6 or later)
is installed.
This applies even if you never use the browser by itself.
Requirements
Does ODYSSEY work with Internet Explorer 7?
Yes, starting with release 2.0.1, the Windows version of ODYSSEY works with Microsoft's new Internet Explorer 7.
Older releases do not work with IE 7.
Requirements
Doesn't the fact that the program uses a web browser mean that it is an online application?
No, except for a single situation, 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:
-
Insert the ODYSSEY CD-ROM into your CD drive,
installation should begin automatically.
If installation does not begin automatically:
-
Open My Computer.
-
Open the disc image for your CD drive.
-
Double click on the Setup icon.
-
Read the license agreement and confirm whether you agree or not.
If you do not agree, you cannot continue installation.
-
When prompted, choose Software Key as the activation method.
-
Follow the prompts to complete program installation.
-
When reaching the final activation dialog, enter the 21 digit activation code and choose
Activatethis will activate your software.
(See the FAQ "How do I install using an activation code if I don't have Internet access?"
if you don't have online connectivity.)
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 Windowsthe procedure for the
Macintosh is analogous:
-
Choose Software Key during the installation process
and follow the prompts to complete program installation.
-
When you reach the activation dialog,
click on the Offline button.
Click on Write Request Fileyou will be prompted to specify a
location to write a "Request.txt" file.
Email this file to codes@wavefun.com.
-
Within 24 hours, you will receive a response file named "Request_code.txt"save
this to your Desktop.
-
Open ODYSSEYwhen prompted for activation,
enter the original 21-digit activation code (again).
-
Click on the Offline button, and this time choose
Activate From Filein the resulting dialog point to the
"Request_code.txt" file on your desktop.
-
This will complete the activation processonce your software is
activated you may delete the "Request.txt" and "Request_code.txt" files.
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 Windowsthe procedure for the
Macintosh is analogous:
-
Do not plug in the USB key prior to installation.
-
Insert the ODYSSEY CD-ROM into your CD drive,
installation should begin automatically.
If installation does not begin automatically:
-
Open My Computer.
-
Open the disc image for your CD drive.
-
Double click on the Setup icon.
-
Read the license agreement and confirm whether you agree or not.
If you do not agree, you cannot continue installation.
-
If prompted to choose a licensing option, select Hardware Keythis will
include the drivers necessary for your computer to recognize the USB key in the
installation procedure.
-
Follow the prompts provided by the installation wizard to complete installation.
-
Plug in the USB key and run the program.
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:
-
Go to
Control Panel
Display
Settings
Advanced
Troubleshoot.
-
Set the "Hardware Acceleration Slider" to the highest setting that still allows the program to run properly
Installation
How do I uninstall the Windows version?
To uninstall the Windows version of ODYSSEY:
-
Use the Uninstall shortcut in the ODYSSEY program group that is found in
Start
All Programs.
If the Uninstall shortcut in the ODYSSEY program group is not available:
-
Use the Start Menu
Control Panel
Add or Remove Programs dialog.
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 (release 2.0 and up):
Vertical separators (between Build/Cell/Plots area, Model area, and Text area):
-
Position cursor on boundary between tiles, click, and drag
Horizontal separator (between Model area and Properties area):
-
Position cursor on the line just below the "Start/Stop" button, click, and drag
User Interface
How do I change the size of the text?
In the Windows version, the text size can be altered
independent of the screen resolution.
If you have a mouse with a scrollwheel, check whether the following works:
-
Click on the white background of one of the ODYSSEY text
panels.
-
To scale the text size, roll the scrollwheel while holding down either the CTRL
key or the CTRL+SHIFT keys (depends on the machine configuration).
ODYSSEY will remember the new setting the next time you start the
program. While the technique above does not work on all computers,
the following will always work on Windows machines:
-
Bring up Internet Explorer (i.e., not ODYSSEY).
-
From the View menu (IE 6) or the Page menu (IE 7), select Text Size
desired setting.
For most computer displays, a text size of either Medium or Smaller
will provide the most efficient formatting.
-
Close Internet Explorer.
In the Macintosh version,
you must change the screen resolution in order to change the text size:
-
Use the {Apple menu}
System Preferences
Hardware
Displays dialog.
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 tool bar similar to the one seen in SPARTAN?
To display a toolbar with icons for the Select modes and the various Build operations including Minimize:
-
From the View menu, select Toolbar.
Note: In the Windows version, the menu item is accessible from any page, including the initial page.
In the Macintosh version, a page with a molecular model must be open.
User Interface
Does clicking on the Refresh/Reload icon only affect the currently displayed model or page?
No, while clicking on the refresh icon takes you back to the subpage that you were on,
it refreshes all models and all subpages of the current experiment.
(Experiments in other tabs are unaffected by a refresh.)
In the Macintosh version, a Reload option is available in the
shortcut (right-click) menu when the cursor is within the text area. However, the effect of this reload is limited:
It only refreshes the HTML of the current subpage, i.e., it does not refresh the molecular model and it
does not refresh other subpages.
User Interface
Can I suppress the text panels of Experiment/Stockroom pages?
To temporarily hide the text panel of the current page:
-
In the View menu, uncheck Text
(or click on the model background, right-click, and uncheck Text).
To permanently hide the text panels of all pages
(Instructor's Edition only):
-
From the Tools menu (Windows) or from the
Odyssey menu (Macintosh), select Preferences...
-
Check Presentation Mode (Hide Text)
User Interface
Can I put the program into true Full Screen Mode, similar to PowerPoint?
The Windows version of ODYSSEY can be put into presentation-style full screen mode:
-
From the View menu, select Full Screen (or use the "F11" key)
To exit full screen mode:
-
In the View menu, deselect Full Screen (or use the "F11" key)
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:
-
Default: Coloration by ODYSSEY atom colors
-
Coloration by standard state (gas, liquid, or solid)
-
Coloration by metallic character (metallic, semimetallic, or nonmetallic)
-
Coloration by valence electron configuration (s/p/d/f blocks; noble gases)
User Interface
Where do I declare the charge when I build an ion with the Atomic Model Kit?
ODYSSEY evaluates built structures using common valence rules
and assigns charges accordingly. A tetrahedrally coordinated nitrogen atom, for example,
is "recognized" as carrying a single positive charge. An explicit declaration of the charge is not
required.
If your built molecule is not in the desired charge state,
try to find the molecule (or a similar one) in the program's Molecular Stockroombecause
of custom settings it may be in exactly the charge state that you are after.
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):
-
Position the cursor on the caption, click, and drag
Plotting and Printing
How do I print snapshots of molecular models?
To print a molecular model if no plot is displayed:
-
From the File menu, select Print....
To print a molecular model while plots are displayed at the same time:
-
Deselect all plots by clicking in the left-side plot pane in any "empty" gray area
outside of the plot frames.
-
From the File menu, select Print....
Plotting and Printing
How do I print a plot?
-
Select the plotit has a blue border around if it is selected.
-
From the File menu, select Print....
Plotting and Printing
How do I print the text panel?
Printing of the HTML-formatted text is different for the two versions:
-
In the Windows version, position the cursor inside the text area, then right-click and select Print.
-
In the Macintosh version, click somewhere in the text area, then select
File
Print.
Plotting and Printing
How do I print the properties table?
In the Windows version, use the computer's screen-capture facility
(many machines have a special "Print Screen" key):
-
Paste the screen shot into any picture editing program.
-
Using the editing features of the picture editing program, crop the screenshot
around the Table of Properties.
-
Print the cropped picture directly from the picture editing program.
In the Macintosh version, the "Properties" table can be printed directly from ODYSSEY:
-
Click somewhere within the Properties table.
-
From the File menu, select Print...
Plotting and Printing
How do I print the entire screen?
-
Use the screen-capture facility of your computermany machines have a special
"Print Screen" key.
-
Paste the screen shot into any picture editing program.
-
Print directly from the picture editing program.
Plotting and Printing
How can I suppress the Windows "Blocked Content" message bar when printing PDF-formatted worksheets?
-
Open Internet Explorer
-
Select Tools
Internet Options...
-
Select Advanced tab
-
Scroll to Security section
-
Check Allow active content to run in files on My Computer
-
Close Internet Explorer
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:
-
Hyperlinking individual models (no accompanying text included)
-
Hyperlinking ODYSSEY's initial page
-
Hyperlinking experiments or stockroom pages (as they appear in ODYSSEY)
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.
General Note:
When you run PowerPoint and use ODYSSEY hyperlinks,
be sure to close ODYSSEY before moving back to PowerPoint
(or you will soon run out of compute power as each new hyperlink will open ODYSSEY again).
Classroom Use
How do I hyperlink an individual molecular model?
-
Save the model that you want to hyperlink as an .xodydata file in a folder of your choice.
Note that "surface data" such as electron densities, potentials, and orbitals will be lost
(
link through the initial page to access such models).
-
Windows:
Before you can hyperlink the file into your PowerPoint presentation,
you must "register" the .xodydata file extension with the Windows operating system
(only this way PowerPoint will know that it needs to start ODYSSEY on encountering your hyperlink):
-
Try to directly open the .xodydata file by double clicking on its icon.
If ODYSSEY starts up and the model displays, you don't need to do anything else.
Move on to item 3).
-
If ODYSSEY doesn't start up, right-click on the .xodydata file and select Open With....
In the ensuing dialog, navigate to the ODYSSEY folder and select "OdysseyStudent.exe" (Student Edition) or "OdysseyInstructor.exe" (Instructor's Edition).
In most cases, you will find the ODYSSEY folder in the "Program Files
Wavefunction" folder of "Local Disk (C:)"
-
Check off the "Always Open With This Program" option (this creates a registry entry).
-
Open the file, then close ODYSSEY.
-
Creating the hyperlinks in PowerPoint:
-
Windows:
Use the "Hyperlink" attribute
and navigate to the location of your saved .xodydata file.
-
Macintosh:
Use the "Action Settings" attribute (i.e., do not use the "Hyperlink" attribute).
In the drop-down menu for "Hyperlink to", select "Other File..."
and navigate to the location of your saved .xodydata file.
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 model via that hyperlink:
-
In your PowerPoint slide, select the object that you wish to hyperlink.
-
Right-click and select Action Settings.
-
Select Run Program and browse for the name of the ODYSSEY executable:
-
Windows:
The executable in the ODYSSEY folder
is either "OdysseyStudent.exe" (Student Edition)
or "OdysseyInstructor.exe" (Instructor's Edition).
In most cases, you will find the ODYSSEY folder in the "Program Files
Wavefunction" folder.
-
Macintosh:
The executable is
either "Odyssey [Version Number] Student.app" (Student Edition)
or "Odyssey [Version Number] Instructor.app" (Instructor's Edition).
In most cases, you will find the file in the "Applications" folder.
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 or .splink file in its original
location in the ODYSSEY foldera copy of the file somewhere else will not do.
-
Windows:
Create hyperlinks for experiments by going through the
ODYSSEY folder
that is installed (in most cases) in the "Program Files
Wavefunction" folder of "Local Disk (C:)."
Find your .odyssey or .splink file
within the "html" subfolder (the general organization is similar to that of an introductory chemistry textbook):
html
Text
{chapter}
{experiment}
For example, the path for the .odyssey file that is associated with the "Liquid Water" experiment is:
html
Text
Liquids Solids
Water.odyssey
.splink files are used for models that include "surfaces" such
as the electron density or molecular orbitals.
For example, the path for the file that is associated with the "Structure and Acidity" experiment is:
html
Text
Acids Bases
Structure and Acidity
Structure and Acidity.splink
Create the hyperlinks in your PowerPoint slides using the "Hyperlink" attribute.
-
Macintosh:
Follow essentially the same protocol as for Windows, but go through the
Odyssey Hyperlinks folder.
To create this folder (you only need to do this once):
-
Download the
MakeOdysseyHyperlinkFolder.sh
file from the Wavefunction web site.
-
Open a Terminal window.
-
Drag the icon for the MakeOdysseyHyperlinkFolder.sh file into the terminal window.
-
Drag the Odyssey .app icon from its permanent location (usually the "Applications" folder) into the terminal window.
-
Make sure that the terminal window is selected, then press the Return key.
Important: Create the hyperlinks in your PowerPoint slides using the
"Action Settings" attribute, i.e., do not use the "Hyperlink" attribute.
In the drop-down menu for "Hyperlink to", select "Other File..."
and navigate to the location of the .odyssey or .splink file.
-
Hyperlinks for stockroom pages can be created in an analogous way, except
that you need to
find your .odyssey or .splink file
within the "archive" subfolder:
archive
{stockroom page}
For example, the path for the .odyssey file that is associated with the "Ammonia" stockroom page is:
archive
Ammonia!Inorganic.odyssey
The .splink file associated with the stockroom page for the "Atomic Orbitals of Argon" is:
archive
Argon...!AOrbitals.splink
Note: Only .odyssey and .splink files with exactly one exclamation mark in the filename can be linked.
-
Under Windows you must "register" the .odyssey and/or .splink file extension with the Windows operating system
for the hyperlinks to work:
-
Try to directly open the .odyssey or .splink file by double clicking on its icon.
If ODYSSEY starts up and the model displays, you don't need to do anything else. Move on to item 3).
-
If ODYSSEY doesn't start up, right-click on the .odyssey file and select Open With....
In the ensuing dialog, navigate to the ODYSSEY folder and select "OdysseyStudent.exe" (Student Edition) or "OdysseyInstructor.exe" (Instructor's Edition).
-
Check off the "Always Open With This Program" option (this creates a registry entry).
-
Open the file, then close ODYSSEY.
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):
-
Open PowerPoint.
-
Select Tools
Options...
-
Select Security tab.
-
Click on Macro Security....
-
Select Low as the security setting.
-
Click OK.
-
Click OK.
-
Close PowerPoint.
-
Open any folder.
-
Go to Tools
Folder Options...
-
Select File Types tab.
-
Scroll to and select the XODYDATA extension
(or ODYDATA if you are using that file type).
-
Click on Advanced.
-
Uncheck Confirm open after download.
-
Click OK.
-
Click Close.
-
Close the open folder.
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:
-
Save the corresponding molecular model
(normally as an .xodydata file) to the needed location.
-
Run the corresponding simulation live, with full access to all visualization and system manipulation
features of the ODYSSEY interface.
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?
Generalizing the approach of conventional plastic model kits,
ODYSSEY provides building blocks and tools for the construction
of a great variety of molecules and systems.
While some of the tools imply certain constraints
(e.g., the building block "tetrahedral" carbon obviously implies that there is
a bias towards 4 single bonds around a carbon atomas opposed to either 3 single bonds or 5 single bonds),
the student is, strictly speaking, not prevented from building chemical "nonsense" structures.
Of course, the same is true for plastic model kitsand also for drawing Lewis structures on a piece of paper!
In essence, ODYSSEY empowers the student to learn chemical rules
in an open-ended, active format. 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 nothing but the memorization of rules.
Classroom Use
How can I assess student work carried out with ODYSSEY?
ODYSSEY includes more than 40 different worksheets
that are included as PDF files with every copy of the program.
In the Instructor's Edition, the worksheets are also available as editable WORD files.
Assessment can be carried out in several different ways:
-
Along the lines of conventional lab reports and homework assignments, students
can fill out copies of the worksheets that they have printed out directly from the program.
-
The teacher creates custom copies of the WORD-formatted worksheets (including all desired changes)
and prints them out.
The students fill out the paper copies that they have received.
-
The teacher makes his/her custom copies of the WORD-formatted worksheets
available to the students in an electronic form (on a class website or server computer).
The students add answers by editing the WORD files on their own computers.
-
If an online homework system is available, the teacher can formulate questions and
assignments using that system. Students work with ODYSSEY
while entering their answers into the computer's online homework system.
Molecular Visualization
Can I depict lone pairs?
To display a schematic representation of lone pairs (where applicable):
-
From the Model menu, select Lone Pairs.
Note: For models 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 Model 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 models 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:
-
From the Model menu, select Ribbons (if the entry does not
appear in the menu, then the underlying file does not contain the
necessary residue information).
-
Also from the Model menu, select Customize...
-
In the "Ribbons" section set the "Coloring" to By Residue.
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 soliddespite 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 anythingthe 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 any molecules that fall right on the boundaries are shown
with some of their atoms still on one side,
while the molecule's remaining atoms are already shown re-entering on the other side.
If desired, you can turn this type of clipping off so that the molecules always seem to
"leave" and "re-enter" the simulation cell as complete entities
rather than with clipped bonds:
-
From the Tools menu (Windows) or from the Odyssey menu (Macintosh), select Preferences...
-
Uncheck (deselect) Periodic Boundary Clipping.
Note that the clipping preference only affects the visualization of molecular systemsthe
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 overriden by the preference setting.
Molecular Visualization
Why do many models of liquids and solids contain one molecule that looks "different"?
For the purpose of highlighting, ODYSSEY often shows one
(arbitrarily selected) molecule in a different model style.
For liquids, for example, the highlighted molecule is typically
shown Space Filling so as to give an idea of the true shape of the molecule.
The "background" of other molecules, however, is typically shown in the Wireframe
or Tube style so as not to clutter up the picture with an abundance of large spheres
for each and every atom.
Molecular Visualization
Can I show two models at the same time?
Comparing systems, situations, and scenarios is one of the most effective teaching techniques.
ODYSSEY facilitates comparisons
of molecular systems in several ways.
-
Comparison of molecules that were self-built:
-
Build the first molecule using the Entry-Level, Advanced, or Peptide build panel.
-
Use the "Insert" feature to start building the second molecule (double click on the background).
-
If you are in Build
Add mode, you can move the two molecules independently (one at a time)
by holding down the CTRL key while dragging the mouse.
(If you are not in Build
Add mode, the two molecules can only be moved as one large unit.)
-
Comparison of simulation cells that were self-built:
-
Build the first simulation cell by making use of the Build and Cell panels.
-
Open a second model kit by selecting File
New.
Build the second simulation cell as desired.
-
Go back and forth between the two systems via the "browser tabs" for the two systems.
(Showing both models directly side by side is not supported because running multiple
simulations at the same time would be very impractical for complex systems.)
-
Comparison of any systems (molecules or simulation cells)
from the same page of the Molecular Stockroom:
-
Go back and forth between the systems using the radio buttons on the page.
-
Comparison of any systems (molecules or simulation cells)
from different pages of the Molecular Stockroom:
-
Retrieve the first system from the Molecular Stockroom.
-
Retrieve the second system from the Molecular Stockroom.
-
Go back and forth between the two systems via the "browser tabs" for the two systems.
Molecular Visualization
What can I do if the graphics performance is poor, particularly when using the
"Space Filling" model style?
On Windows computers, you can try the following:
-
In the Tools menu, select Preferences.
-
Check off Reduced Graphics for Slower Machines.
Click OK.
Molecular Visualization
What can I do about unsatisfactory graphics performance when running on battery?
On Windows computers, you can try the following:
-
In the Tools menu, select Preferences.
-
Check off Reduced Graphics for Slower Machines.
Click OK.
Physical Properties
How do I measure physical properties?
To query the numerical values of physical properties:
-
From the View menu, select Properties
-
From the Properties menu,
select the desired property, such as Atom
Electronegativity
-
If a selection is required, then this is indicated in the column to the right
of the properties list; e.g., adding Mole Fraction to the list necessitates
a Select Group action.
Physical Properties
How do I change the physical units?
To change the default settings:
-
From the Tools menu (Windows) or from the Odyssey menu (Macintosh),
select Preferences...
-
Adjust the radio buttons within Units to reflect your desired 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:
-
Click (Windows) or double-click (Macintosh) the numerical value field for the property in the "Table of Properties" and enter your desired value
(excluding units).
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 molecule?
To minimize the energy of any molecule or any other system in vacuum:
-
From the Build menu, select Minimize.
Note: Minimization of liquid and solid structures is not available.
Physical Properties
How are the energies calculated?
For each molecular model, 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 complicatedthere 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:
-
Intermolecular attractive energy:
an energy term that represents Van der Waals forces (dispersion forces) between non-bonded atoms.
-
Intermolecular repulsive energy:
a steeply repulsive energy term for steric interactions at short distance
that makes a close "overlap" of non-bonded atom very unlikely.
-
Coulomb energy (both inter- and intramolecular):
energy term due to the assignment of "effective charges" to all the atoms of a molecule;
at the intermolecular level, this energy represents charge-charge, charge-dipole, and dipole-dipole interactions.
-
Repulsive interactions between the molecules of the system and the confining walls (if there are any).
-
Intramolecular energy of bond-stretching:
the spring-like energy that it takes to distort a bond from its equilibrium bond distance.
Note: This energy term (and sometimes also the following one) does not vary over time
if ODYSSEY keeps the molecular geometry "rigid."
-
Intramolecular energy of angle-bending:
the energy that it takes to distort any three bonded atoms from their preferred bond angle.
-
Intramolecular energy of rotation around dihedral angles:
a periodic function that describes the relative energies of the various "staggered" and "eclipsed" conformations of
any four consecutively bonded atoms.
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:
-
If thermodynamic tables give standards heats of formation as a function of temperature,
the assumed reference state is temperature dependent
(because the enthalpy of formation of the stable phase of an element is by definition zero for all temperatures).
-
If thermodynamic tables give (H°H°298) data, then the implied reference state changes from phase to phase and from substance to substance.
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:
-
If thermodynamic tables give standard free energies as a function of temperature,
the assumed reference state is temperature dependent
(because the free energy of the stable phase of an element is by definition zero for all temperatures).
-
If thermodynamic tables give (G°G°298) data, then the implied reference state changes from phase to phase and from substance to substance.
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:
-
The partnering atoms must involve a known hydrogen bond donor
and a known hydrogen bond acceptor.
Oxygen, nitrogen, and fluorine are the most important formers of hydrogen bonds, but not necessarily in all valence states.
In liquid water, for example, sp3 oxygen acts as both a donor and an acceptor of hydrogen bonds.
The sp2 oxygen of carbonyl groups, however, can only act as an acceptor and must pair up
with some other donor if it is to form a hydrogen bond.
-
The distance between the hydrogen atom and the acceptor atom has to fall within a range of 122-260 pm.
-
Overtly bent hydrogen bonds are excluded by requiring that the angle
∠(hydrogen atom-donor atom-acceptor atom) is smaller than a set value.
For water and ammonia this angle is 30°, for hydrogen fluoride it is 86°.
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 modelsnot 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 modeling 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:
-
From the View menu, select Properties.
-
From the Properties menu,
select Dynamics
Speed.
-
Compare the speed data for the liquid phase (low temperature)
and gaseous phase (high temperature) of the same substance.
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:
-
Retrieve a sample of liquid from the Molecular Stockroom, or build one
yourself using the Atomic Model Kit (you will need to know the density of the desired liquid).
-
From the View menu, select Properties.
-
From the Properties menu,
select first Thermodynamics
Temperature
and then
Thermodynamics
Volume.
-
Start the simulation.
-
Overwrite the Volume Field by a number that is at least 100 times bigger than the number shown.
-
Resize the simulation cell: Edit
Resize.
-
Increase the temperature with the slider provided to speed up the process of evaporation.
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 gravity does not make a difference for molecular-sized samples.
A number of very familar phenomena, however, crucially depend on the presence of gravitational forces.
Such phenomena include the flow of liquids and, more generally, the formation of "neat" interfaces.
Basically, the behavior observed in ODYSSEY simulations closely mimics
that of macroscopic samples in the absence of gravity (such as on any 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:
-
From the View menu, select Properties.
-
From the Properties menu,
select first System
Density
and then
Thermodynamics
Volume.
-
Adjust the volume with with the provided slider so as to reach the desired 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:
-
Covalent bonds are being broken or formed.
-
The time scale of the process in question does not fit within the typical picosecond (1012 sec)
time range that is accessible to the program.
The dissociation of strong acids falls into the first one of these categories.
If desired, models of the dissociated speciessuch as (Cl)aq and
(H3O+)aq,
(H5O2+)aq, or
(H7O3+)aqcan
be built with ODYSSEY's Atomic Model Kit.
Physical Behavior
If I have a sodium chloridewater 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:
-
Covalent bonds are being broken or formed.
-
The time scale of the process in question does not fit within the typical picosecond (1012 sec)
time range that is accessible to the program.
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
(such models can be found in ODYSSEY's Molecular Stockroom).
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 models be saved?
Yes, the currently displayed model can always be saved as an .xodydata file
(or .odydata file) into
locations outside of the ODYSSEY folder (the
ODYSSEY folder is Read Only in order to
preserve the integrity of the software):
-
From the File menu, select Save As...
-
Navigate to the desired location, select a filename, and save the file.
-
The saved model is shown in a new browser tab.
The following restriction applies when saving models:
-
"Surface" information (Orbitals, Electron Density Distributions, Electrostatic Potentials, Electrostatic Potential Maps)
is not saved.
Importing / Exporting / Annotating
In what format should three-dimensional models 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 with ODYSSEY, but not be saved).
The alternate .odydata format is needed for two purposes:
-
For a potentially considerable speed-up when opening large modelson many machines it is advantageous to use the
.odydata format for saving and reopening models of more than ~1,000 atoms
-
For saving files that can be read with SPARTAN
Importing / Exporting / Annotating
Can I open saved models with "drag and drop"?
Starting with release 2.1, all ODYSSEY files
(.xodydata, .odydata, 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 models be saved?
Yes, screen shots of molecular models can be saved in several formats:
-
From the File menu, select Save Image As...
-
Choose a file name and one of the following file types:
-
.jpg (Windows and Macintosh)
-
.png (Windows and Macintosh)
-
.bmp (Windows only)
-
Save the graphics file of the model to the desired location.
Tip: For best resolution, hide the text panel (in the
View, uncheck
Text)
prior to saving the screenshot.
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)
as well as .spartan files
(generated by Wavefunction's program SPARTAN).
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 Experiments and
most of the pages in the Molecular Stockroom can be individually annotated:
-
Click on the Windows "document" icon (looks like a piece of notebook paper)
at the top of the text panel.
This opens a
Notes page that accepts any text that is entered.
-
Return to the originating page by clicking on the Save+Exit link
(or a similarly named link in earlier releases of the program)
at the bottom of the Notes page.
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?
Customization of ODYSSEY content
can be carried out in the following ways:
-
In the Instructor's Edition of the program,
all student worksheets are available as MS Word files that can easily be edited.
-
ODYSSEY's annotation capability (see FAQ "Can I annotate the text pages?")
allows to add brief custom comments to all
Experiments and to most of the pages in the Molecular Stockroom.
The text portion of ODYSSEY is HTML formatted
and can in principle also be edited.
However, technical expertise is required as technologies other than HTML are involved.
Also, Wavefunction's copyright must not be infringed.
Adding entirely new topics and new pages to ODYSSEY's content portion is not supported.
Please contact Wavefunction with suggestions for incorporation of new content into future releases of the program!
© 2004-2008 Wavefunction, Inc.