Getting Started Using Cranium
Applicability: Cranium (core version 0315+)
Welcome to Cranium !
Cranium is our physical property management and estimation
software package. With Cranium, you can store physical
property data, generate physical property estimates,
capture property estimation knowledge,
and diseminate property knowledge into reports, graphs,
websites and other chemical software programs.
This page provides a quick tour of some of Cranium's capabilities.
Because you will be creating new entities, entering data
and estimating properties, it is very important that you
create and use a copy of a knowledge base.
Tip: No copying needed in Reader version
The Reader version of Cranium does not allow you to make copies of documents.
If you are using the Reader version you can edit the original document. The
Reader version does not save any changes.
Example: Create a copy of a knowledge base
Start the Cranium application. Cranium displays a welcome dialog.
Press the welcome dialog’s Done button. Cranium will then
display the Open file dialog.
Select a knowledge base and press the Open button. You can choose
any of the knowledge bases that come with the Cranium
application. Cranium will open and display the selected
Choose the 'Save a Copy' command from the File menu. Cranium
displays the Save As dialog.
Choose a location and enter a name for the knowledge base
copy, e.g., "MKS Core Knowledge Base - Work".
Finally press the dialog’s Save button.
Cranium will save a copy of the current knowledge base. Use the File
menu's Open command to open this new copy.
The 'mkskbd' extension denotes a Molecular Knowledge
Systems Knowledge Base document.
Tip: Use Save Copy command to make backups
The Save a Copy command is useful for quickly making a
backup of your current document. Before you make significant
changes to a document, you should consider using the Save a
Copy command to make a backup.
A knowledgebase is a compilation of information on elements,
molecular structures, chemicals, mixtures, estimation techniques
and references. Values for the properties of each entity are
presented on a single "page" of the knowledge base. These entity
pages are arranged into "chapters". The tabs at the top of each
knowledge base window correspond to each of these chapters.
Since each entity is displayed on a separate page in a chapter,
navigating through Cranium primarily involves changing chapters
and turning pages. See documentation for the
Navigation Menu for more details
on navigation. For more details on the structure of a Cranium
Example: Change to the Chemicals Chapter
Click the left mouse button on the Chemicals Chapter tab located
at the top of the window. Cranium displays a page of the
Click on a tab at the top of a window to change
Example: View chemicals on other pages
The navigation controls located in the toolbar enable you to page
through all the entities within a chapter.
Move to the chapter's first page.
Move to the chapter's previous page.
Move to the chapter's next page.
Move to the chapter's last page.
Press the toolbar’s right facing, hollow arrow or choose the
Navigation menu’s Page Forward command or press the ctrl-f
accelerator keystroke. The ctrl-f keystroke is generated by
holding down the control key and then pressing the 'f' key.
All three methods are equivalent and result in the display of the
next chemical stored in the knowledge base. Navigating to the
previous chemical is done by either pressing the toolbar’s left
facing, hollow arrow, choosing the Navigation menu’s Page Back
command or pressing the ctrl-B accelerator keystroke.
At a chapter’s first page, the commands for paging backward will be
disabled. Likewise, at the chapter’s last page, the commands for
paging forward will be disabled.
Example: Go to the page displaying a specific chemical
Choose the Navigation menu’s Goto command or press ctrl-g. Cranium
displays the Go To Chemical dialog. (See documentation for the
All Entities Dialog for more
details on the Go To dialog.)
Attribute, e.g., identifier, synonym, etc., displayed
List of entities containing the selection substrings
Only entities containing this substring
Only entities containing this substring
Type ‘ethyl’ into the first Match Substring edit control and
'hexano' into the second edit control. (Note: leave off the
'l' at the end of hexanol for this example.) Only entities
containing those substrings are displayed. Scroll through the
displayed list and choose 2-ethy-1-hexanol. The application turns
to the page displaying 2-ethy-1-hexanol’s properties. (If you
chose to work with another knowledge base that does not contain
2-ethy-1-hexanol, simply choose another chemical.)
Estimating Chemical Properties
One of Cranium’s key capabilities is to estimate physical properties
quickly, easily and accurately. To estimate a property Cranium first
collects all applicable techniques, sorts them by accuracy, and then
tries each one until an estimate is generated.
Example: Estimate 2-ethy-1-hexanol's physical properties
Choose the Compute Estimates command from the Commands menu.
The application displays the Property Estimation Dialog.
Press the Start button. The application will now estimate each
property documenting its progress in the dialog.
Once all estimates have been generated, expand the Boiling Point
node, by clicking on the 'plus' sign to the left of the property,
and continue to expand all child nodes. The display should appear
similar to the following.
This figure shows that the knowledge base has three estimation techniques
that can estimate the boiling point. The first technique tried was the
'Tb: Antoine Equation – PGL2001 [MKS]' technique. This technique failed.
The second technique was the 'Tb: Stein + Brown Method [MKS]' technique.
This technique succeeded – its estimate is reported
at the end of the listing. The third technique was the 'Tb: Joback Method [MK
S]' technique. This technique was not tried because an estimate
had already been generated.
Click the left mouse button on the 'Tb: Antoine Equation – PGL2001 [MKS]'
technique. The dialog’s
Details button will become active.
Press the Details button. Cranium displays the Detailed Estimation Results
The dialog shows that the 'Tb: Antoine Equation – PGL2001 [MKS]' technique
failed because it did not have the needed parameters for 2-ethyl-1-hexanol.
Control showing the detailed results of the estimation.
Press the Done button to return to the Property Estimation Dialog.
Press the Property Estimation dialog’s Save button. Cranium stores
the estimates in the current knowledge base and displays them on
Cranium automatically selects the best applicable estimation technique.
At times you may wish to manually specify which technique Cranium should
use for a particular property.
Column of data values.
Column of estimated values.
Example: Manually specify the boiling point estimation technique
Click the left mouse button on the boiling point field's
estimate control. Cranium displays the Estimation Details
dialog. This dialog shows the estimated value, the technique
used to generate the estimate and comments.
Make a mental note of the estimation tehnique used and then
click the dialog's OK button to close the dialog.
Click the right mouse button on the boiling point field’s estimate
control. Cranium displays the control’s command menu.
Choose the Select Technique command from the menu. Cranium displays
the Estimation Technique Information dialog. The property’s estimation
mode is currently set to Automatic Mode. In Automatic Mode Cranium
selects the best applicable technique.
Change the Estimation Mode to Manual Mode and select the
Joback Method. (Note: the actutal techniques used and
available may differ depending upon the knowledge base
you are using. The key concept for this example, is to
choose a different technique than the one Cranium
Press the dialog's OK button. Cranium will now use the Joback Method
the next time it estimates the normal boiling point.
Note 2-ethyl-1-hexanol's currently estimated boiling point. Use
the previous procedure to estimate the chemical’s
properties again. Note how the
boiling point estimate has changed.
Example: Estimate the vapor pressure at several temperatures
Cranium also estimates temperature and pressure dependent properties.
To estimate such dependent properties, you must first enter
temperature and pressure values.
Scroll down to the data pane’s Temperature Dependent section.
Values type control.
Field's table control.
Click the left mouse button in the property control, i.e., the
control to the right of the "Property:" label. Cranium
displays the Properties dialog. This dialog lists all the
temperature dependent properties currently known to Cranium.
Properties list control.
Values type control.
Select Vapor Pressure, Liquid – f(T) in the Properties list
control and Estimates from the Values Type control. Then
press the OK button.
You must now enter the temperatures for which you want estimates
Click the left mouse button within the Temperature Dependent field's
table. Click in the white, grid area of the table not in the
column headings or row labels. Cranium displays the state variables
Double click the left mouse button in the table’s first row. Cranium
displays another edit dialog. Enter a value of 298 K in this dialog
and press the OK button.
Click and hold the left mouse button in the table's second row. Cranium
will highlight the row.
Drag the mouse downward to the fifteenth row and release the mouse
button. Rows two through fifteen will now be highlighted.
Press the Series button. Cranium will display the Temperature
Enter 100 C for the Starting temperature. Change the temperature
option to Temperature Increment and enter a value of 5 C. (For
now, if the temperature units are set to a value other than C,
enter the corresponding temperature value in the current units.
See the documentation for the
Set Property Units dialog for details
on changing property units.)
Press the OK button. Cranium will generate a series of temperature
entries starting at 100 C and being incremented by 5 C.
Press the Save button in the edit dialog. Cranium stores the entered
temperatures in the knowledge base and redisplays the Temperature
Dependent field's table.
Temperature dependent estimates can now be generated as done
previously. However, for this example you will only generate vapor
Click the right mouse button within the Temperature Dependent
field's table. Click in the white, grid area of the table
not in the column headings or row labels. Cranium displays
the field's commands menu.
Choose the Compute Estimates command from the menu. Cranium will
display the property estimation dialog.
Press the Start button. Cranium will estimate the vapor pressure
for each temperature value.
Press the Save button to have Cranium store the estimated values
in the knowledge base.
Example: Add a new chemical
One of the advantages of an electronic reference book over a
printed one is the ease with which pages can be added
Using the tabs at the top of the document, change to the
Chemicals Chapter by clicking the left mouse button on
Press the Add toolbar button (the large plus sign). Alternatively
you can choose the Add Page command from the Edit menu or use
the crtl-a keyboard accelerator.
Add Button: pressing this toolbar button
will add a new, blank page to the current
Delete Button: pressing this toolbar button
will delete the current page from the current
chapter. IMPORTANT: the deletion of a page cannot
Example: Enter a name for our new chemical
Click the left mouse button in the identifier’s field data control.
Cranium displays the Chemical Identifier's edit dialog.
Identifier's field data control.
Type in a name for our new chemical. You can also add a
reference and comments. (See the documentation for the
Text-Reference Edit Dialog for
details on editing.)
Press the Save button. Cranium will store the values in the
knowledge base and display the new name in the chemical's
Editing Molecular Structure
Many estimation techniques require knowledge of a chemical's
molecular structure. Some techniques require only information
about the chemical's family, e.g., is the chemical chlorinated.
Other techniques, e.g., group contribution techniques, require
a chemical's structure to be completely dissected into molecular
Cranium uses a simple connectivity model to represent molecular
structure. Atoms and bonds are connected into a simple graph.
Example: Enter a molecular structure for our new chemical
Scroll the data pane to the Chemical Structure section, located
near the top of the pane, and click the left mouse button in
the Structure field. Cranium displays the molecular structure
The tool buttons on the dialog's left are used to change
drawing modes. The controls at the dialog’s top are used to
specify the current element and the current bond type. The
large central window is the canvas on which you draw your
Press the Atom button (the large A). Cranium now adds an
atom wherever you click the mouse in the canvas pane.
Move the mouse onto the canvas pane and click the left
mouse button several times in several different locations.
Cranium creates and adds several new carbon atoms.
Cranium uses the current element, specified at the dialog's top,
to create new atoms at the location of your mouse click. Click
the left mouse button on the elements control. Choose Oxygen from
the list of available elements.
Click the left mouse button on the canvas pane to add a new
As you add each atom, Cranium adds the appropriate number of assumed
hydrogens. Cranium automatically updates the number of assumed hydrogens
as you bond atoms together.
Press the Bond button (the diagonal line). Cranium is now ready
to create bonds between atoms.
Click the left mouse button on the first atom to be bonded. Cranium
redraws the atom in green and surrounds it with four small,
Click the left mouse button on the second atom to be bonded. Cranium
creates a bond of the currently selected bond type and attaches it
to this atom and the first bonding atom.
The current bond type is changed using the bond type control located
at the top of the dialog. Click the left mouse button on the bond
type control. Cranium displays a list of available bond types.
Choose the Double Bond type from the list.
Continue the process, selecting pairs of atoms to bond, until all
atoms are bonded.
You have now completed editing your new structure. Press the Save
button. Cranium will store the structure in the knowledge base and
redisplay it in the structure field. (See documentation for the
Structure Edit Dialog for details on
editing molecular structure.)
You can now use the Commands menu Compute Estimates command to estimate the
properties of the new structure.