Molecular Drawing Tool

The Molecular Drawing Tool lets you create questions that require students to draw molecules online, and select and edit parts of molecular drawings you provide. The tool uses the solutionAppletFlash answer type.

Note: Alternatively, you can use the newer Lewis Structure Drawing Tool for students to draw Lewis structures and/or to select and edit parts of Lewis structure drawings you provide. For instructions on Organic Chemistry answer types (solutionOchemSkeletal and solutionOchemMechanism) that use the MarvinSketch drawing tool, see the release notes.

 

Requirements

To use the Molecular Drawing Tool, you need:

• The Adobe® Flash® Player
• moldraw5_authoring_2011.html, the Molecular Drawing Tool file
• moldraw5.swf, the Flash applet for molecular drawings

Important: To receive the latter two files, contact Mastering Support. Be sure to save both files to the same folder. The drawing tool won't work if they're in separate folders.

Overview

1. Set up the molecular drawing answer.
2. Specify drawing parameters in the Molecular Drawing Tool.
3. Copy drawing tool parameters into the answer box.
4. Create correct expressions, correct answers, and wrong answers.

Optionally, if you want atoms or molecules to display on the grid by default, you can create an xml file and add it to your assets. For details, see Creating assets that contain atoms or molecules.

The next sections provide details. For examples of using the tool, see Chiral molecular drawing example and Select atom example.

Note: Do not use this tool for complex ions since it doesn't handle brackets or ligands.

Set up the molecular drawing answer

1. Create a new item for the drawing.
   
   
2. Under Value in the answer box, right-click and remove the solutionMultipleChoiceRadio answer type.
3. Click add and select solutionAppletFlash.
4. In the new answer box displayed, enter moldraw5.swf beside Applet Name.

Specify drawing parameters in the Molecular Drawing Tool

1. Open the Molecular Drawing Tool, moldraw5_authoring_2011.html, in a browser that has the Flash plugin.
   
   
   
   
   
   
2. Set the grading options for the problem on the right.
   
   
   
   An open circle indicates that the option will be graded, while a hash mark through it indicates that it won't be graded. Click an option to toggle whether or not it will be graded.
   
   

		Grade hydrogen atoms
		Grade cis/tran isomers
		Grade chirality
		Grade lone pair electrons

3. Set how students will complete the problem by clicking the button in the upper right, labeled both by default, and selecting both (enables both drawing and selecting), draw, or select.
   
   

Note: The name of this button changes, reflecting the last choice made.

Copy drawing tool parameters into the answer box

1. Right-click the drawing grid and select get parameters.
2. In the Parameters box, press Ctrl + V to paste the drawing’s parameters, which appear as codes. (See Parameter codes for descriptions.)

Note: You no longer need to add a URL to the end of the parameters.

3. Enter the Width and Height for the drawing.
4. Create correct expressions, correct answers, and wrong answers.

Parameter codes

These codes are automatically entered into the answer box when you paste parameters from the Molecular Drawing Tool. This table is for reference only (1 = graded, 0 = not graded).

Code	Meaning
Qtype=	draw – The part involves drawing only. both – The part involves both drawing and selecting. select – The part involves selecting only.
Hydrogens=1	Students must include all hydrogen atoms for a correct grade. The hydrogen grading option pertains only to carbon atoms, since hydrogen atoms are automatically graded for all non-carbon atoms. Whether hydrogen grading is on or off, PF4H requires students to draw the H for a correct answer. If hydrogen grading is off, students can draw CH4 by entering C for a correct answer; drawing CH5 however, would still be incorrect. Hydrogen generally are omitted from the grade for large alkanes or ring structures for which line-bond formulas are appropriate.
Nonbinding=1	Students must include all lone-pair and non-bonding electrons for correct grade. In most cases you will not want to grade based on nonbonding electrons.
Chirality=1	Students must draw a specific enantiomer for a correct grade. In most cases you will not want to grade chirality.
Isometry=1	Student must enter the correct cis or trans isomer to be marked correct. Unless you are dealing with alkenes you will probably not want to grade isometry.
Skeleton=1	The part is in line-bond mode. Only the carbon skeleton with select H atoms and substituents will be shown. Note that H atoms are ‘assumed’ to be present on carbon atoms with less than four bonds. These ‘assumed’ hydrogen atoms will not count toward EZ or RS grading options. Therefore, line-bond mode is incompatible with the grading option hydrogen=1 as well as any molecule with a hydrogen atom attached to chiral atom when RS is graded or a hydrogen atom attached to a carbon of a carbon- double bond when EZ is graded.

 

Create correct expressions, correct answers, and wrong answers

Use the tabs at the top of the Molecular Drawing Tool to create correct expressions, correct answers, and wrong answers, and then copy expressions and answers into the answer box. For a detailed example, see Chiral molecular drawing example.

Note: For molecules with resonance, such as aromatics or the sulfite ion, accept multiple correct answers, one for each resonance structure.

Toolbar button	Purpose	How to use it
Arrow	Moves atoms or bonds within a molecule. You can also change the angle or length of a bond using the arrow tool.	Click the Arrow button. On the grid, click and drag an atom or bond to move it to a new position.
Checkmark	Enables selection of bonds or atoms in a selection question. For example: You might need to answer a question by selecting (i.e., identifying) a particular atom in a provided molecular drawing.	To select individual items: Click the Checkmark button. On the grid, select an atom or bond. The selected item changes from black to green. To select a group of items: Click the Checkmark button. On the grid, click and drag to create a box around the parts of the molecule you want to select as a group.
Bond	To draw bonds between atoms. Default = single bond. Click the down arrow and select a bond type: – Single bond – Double bond – Triple bond – The bond is directed toward you (away from the grid) – The bond is directed toward the grid (away from you)	To connect two existing atoms: Click and drag from the first atom to the second atom. Release the mouse button. To add atoms and bonds at the same time: Click the Bond button. Add an atom by clicking the grid. Select the atom by clicking it, and then add a bond to it by dragging. When you release the mouse button, another atom appears at the other end of the bond. To edit a bond type after you have added it: With the Bond button active, click any bond. If you continue clicking, the bond type cycles from single to double to triple to single, etc.
Atom	To add an atom to the grid. Click the down arrow, and select an element: C – carbon (default) H– hydrogen O – oxygen N – nitrogen S – sulfur P – phosphorous F – fluorine Cl – chlorine Br – bromine I – iodine X – unspecified (i.e., placeholder)	Click the Atom button. The Bond button is highlighted in orange, and the Atom button remains blue. [Optional] Select a different element by clicking the down arrow and selecting one. The button name changes to the element chosen. Click the grid to place the new atom. Place atoms on intersecting points of the background grid – you can't place atoms partially or completely off the screen. To change any element symbol that appears on the grid: Double-click the atom and type the correct element symbol from the keyboard. If you incorrectly type an element symbol: Press the Enter key. The tool attempts to correct the format or element symbol, such as to change “n” to “N”.
Charge	To add or change an atom’s charge. The default charge is 0.	Click the Charge button. On the grid, click the atom to add or change a charge. A black box (with a default value of 0) appears in the superscript position. From the keyboard, type a number and a plus or minus sign. For example, 3-. The plus sign (+) is optional. You can enter the charge before or after the charge value. (The tool reformats the charge sign to the correct position if you enter it in the wrong position.)
Electron dot	To place electron-dot pairs or single electrons on an atom. The default is electron pair. Click the down arrow and select either an electron pair or a single electron.	Click the Electron dot button. Click to add the electron(s) to the atom of your choice. To change the position of electron(s): With the Electron dot button active, click the electron(s), and drag to rotate them around the atom. Important: Adding two single dots in a drawing is not the same as adding an electron dot pair.
Eraser	To delete parts of molecules. To erase all of your work at once: Click the Reset button (described below).	Click the Eraser button. Click a molecule part (bond, atom, charge, or electron) to delete it. Note: If you click an atom with the Eraser button active, any associated bond is also deleted.
Line-bond toggle	To display or hide carbon atoms in a carbon chain. This tool is useful when representing long carbon chains, such as pentane.	Click the Line-bond button to switch between active (orange) and inactive (blue). If you can't deactivate the button when answering a question, line-bond mode is required for the answer. Line-bond mode is incompatible with: The grading option hydrogen=1 Any molecule with a hydrogen atom attached to a chiral atom when RS is graded Any molecule with a hydrogen atom attached to a carbon-carbon double bond when EZ is graded
Reset	Clears the grid to its starting point, whether it was blank or contained portions of a molecule. To delete just a portion of your work: Use the Eraser button (described above).	Click the Reset button to return the grid to its original state.

 

Tips

• To rotate a provided 3D molecule in any direction, click and hold the molecule.
• The active button is orange.
• The identification color for molecular parts you select depends on the active button. If the Arrow button is active, selections are red. If the Checkmark button is active, selections are green.
• For “select” questions, use the Checkmark button to select correct atoms.
• You can’t use copy and paste keyboard commands (Ctrl + C and Ctrl + V) to copy and paste molecular elements on the grid.

Copying expressions and answers into the answer box

The answer string generated depends on the parameters that are set. Make sure the parameters are correct before generating the answer string (with get answer string, described below.

1. When you're done creating the correct expression, right-click the grid and choose get correct expression.
2. In the Item Editor, click add correctExpression and paste (Ctrl + V) the information into the box.
3. In the Molecular Drawing Tool, right-click the grid and choose get answer string.
4. In the Item Editor, paste (Ctrl + V) the information into the Correct Answer(s) box.
5. In the Molecular Drawing Tool, change the molecule as needed for an incorrect answer.
6. Right-click the grid and choose get answer string.
7. In the Item Editor, click add expression beside Wrong Answer(s), and paste (Ctrl + V) the information into the box.

 

See also:

Creating assets that contain atoms or molecules

Select atom example

Chiral molecular drawing example

Grading chiral molecules