diff --git a/docs/en_us/course_authors/source/Images/MoleculeViewer.png b/docs/en_us/course_authors/source/Images/MoleculeViewer.png new file mode 100644 index 0000000000..438a7be033 Binary files /dev/null and b/docs/en_us/course_authors/source/Images/MoleculeViewer.png differ diff --git a/docs/en_us/course_authors/source/Images/Molecule_Editor.png b/docs/en_us/course_authors/source/Images/Molecule_Editor.png index bd9cd0e4e5..d81a018d85 100644 Binary files a/docs/en_us/course_authors/source/Images/Molecule_Editor.png and b/docs/en_us/course_authors/source/Images/Molecule_Editor.png differ diff --git a/docs/en_us/course_authors/source/change_log.rst b/docs/en_us/course_authors/source/change_log.rst index f964dfd510..76312baf56 100644 --- a/docs/en_us/course_authors/source/change_log.rst +++ b/docs/en_us/course_authors/source/change_log.rst @@ -22,6 +22,8 @@ September, 2014 - Removed "These problems only allow integers and a few select constants" from table of problem types in :ref:`Create Exercises`. * - - Added a note about angle bracket characters to the :ref:`Dropdown` topic. + * - 09/26/14 + - Added :ref:`Molecule Viewer` to :ref:`Create Exercises` ************** August, 2014 diff --git a/docs/en_us/course_authors/source/exercises_tools/create_exercises_and_tools.rst b/docs/en_us/course_authors/source/exercises_tools/create_exercises_and_tools.rst index 95ba2f19b5..d69ce4cba9 100644 --- a/docs/en_us/course_authors/source/exercises_tools/create_exercises_and_tools.rst +++ b/docs/en_us/course_authors/source/exercises_tools/create_exercises_and_tools.rst @@ -185,6 +185,11 @@ STEM Exercises and Tools :alt: Example molecule editor problem - :ref:`Molecule Editor` - The molecule editor allows students to draw molecules that follow the rules for covalent bond formation and formal charge, even if the molecules are chemically impossible, are unstable, or do not exist in living systems. + * - .. image:: /Images/MoleculeViewer.png + :width: 100 + :alt: Example molecule viewer + - :ref:`Molecule Viewer` + - With the molecule viewer, you can create three-dimensional representations of molecules for your students to see. * - .. image:: /Images/image292.png :width: 100 :alt: Example numerical input problem diff --git a/docs/en_us/course_authors/source/exercises_tools/index.rst b/docs/en_us/course_authors/source/exercises_tools/index.rst index dae0accdf8..864038d7a2 100644 --- a/docs/en_us/course_authors/source/exercises_tools/index.rst +++ b/docs/en_us/course_authors/source/exercises_tools/index.rst @@ -35,6 +35,7 @@ Course Content Index`. lti_component math_expression_input molecule_editor + molecule_viewer multiple_choice mult_choice_num_input numerical_input diff --git a/docs/en_us/course_authors/source/exercises_tools/molecule_editor.rst b/docs/en_us/course_authors/source/exercises_tools/molecule_editor.rst index f43aba0f18..6be22c6956 100644 --- a/docs/en_us/course_authors/source/exercises_tools/molecule_editor.rst +++ b/docs/en_us/course_authors/source/exercises_tools/molecule_editor.rst @@ -1,14 +1,20 @@ .. _Molecule Editor: -####################### -Molecule Editor Tool -####################### +######################## +Molecule Editor Problem +######################## + +Studio offers two tools that you can use in discussions of molecules: + +* With the **molecule viewer**, you can create three-dimensional representations of molecules for students to view. For more information about this tool, see :ref:`Molecule Viewer`. +* With the **molecule editor**, you can allow students to draw their own molecules. + +Both tools use **JSmol**, a JavaScript-based molecular viewer from Jmol. In addition, the molecule editor problem type uses the JSME molecule editor created by Peter Erl and Bruno Bienfait. (You don't need to download either of these tools; Studio uses them automatically.) For more information about JSmol, see `JSmol `_. For more information about the JSME molecule editor, see `JSME Molecule Editor `_. Students can use the molecule editor to learn how to create molecules. The molecule editor allows students to draw molecules that follow the rules for covalent bond formation and formal charge, even if the molecules are chemically impossible, are unstable, or do not exist in living systems. The molecule editor warns students if they try to submit a structure that is chemically impossible. -The molecule editor incorporates two tools: the JSME molecule editor created by Peter Erl and Bruno Bienfait, and JSmol, a JavaScript-based molecular viewer from Jmol. (You don't need to download either of these tools--Studio uses them automatically.) For more information about the JSME molecule editor, see `JSME Molecule Editor `_. For more information about JSmol, see `JSmol `_. - .. image:: /Images/Molecule_Editor.png + :width: 500 :alt: Image of the molecule editor .. _Create the Molecule Editor: @@ -17,32 +23,12 @@ The molecule editor incorporates two tools: the JSME molecule editor created by Create the Molecule Editor ****************************** -To create a molecule editor, you need the following files: +To create a molecule editor problem: -* MoleculeAnswer.png -* MoleculeEditor_HTML.png -* dopamine.mol - -To download all of these files in a .zip archive, go to http://files.edx.org/MoleculeEditorFiles.zip. - -.. note:: The molecule that appears when the tool starts is a dopamine molecule. To use a different molecule, download the .mol file for that molecule from the `list of molecules `_ on the `BioTopics `_ website. Then, upload the .mol file to the **Files & Uploads** page for your course in Studio, and change "dopamine.mol" in the example code to the name of your .mol file. - -To create the molecule editor that appears in the image above, you need an HTML component followed by a Problem component. - -#. Upload all of the files listed above to the **Files & Uploads** page in your course. -#. Create the HTML component. - - #. In the unit where you want to create the problem, click **HTML** under **Add New Component**, and then click **HTML**. - #. In the component that appears, click **Edit**. - #. In the component editor, paste the HTML component code from below. - #. Make any changes that you want, and then click **Save**. - -3. Create the Problem component. - - #. Under the HTML component, click **Problem** under **Add New Component**, and then click **Blank Advanced Problem**. - #. In the component that appears, click **Edit**. - #. In the component editor, paste the Problem component code from below. - #. Click **Save**. +#. Under **Add New Component**, click **Problem**, and then click **Molecular Structure**. +#. In the component that appears, click **Edit**. +#. In the component editor, modify the code to correspond to your problem. +#. Click **Save**. .. _EMC Problem Code: @@ -50,115 +36,79 @@ To create the molecule editor that appears in the image above, you need an HTML Molecule Editor Code ======================== -To create the molecule editor, you need an HTML component and a Problem component. - -HTML Component Code -*************************** - -.. code-block:: xml - -

Molecule Editor

-

The molecule editor makes creating and visualizing molecules easy. A chemistry professor may have you build and submit a molecule as part of an exercise.

-
- -
-
- -
-
-
Using the Molecule Editor+ open
-
-
- -
-

 

-
-
Are the molecules I've drawn chemically possible?+ open
-
-
- -
-
 
- - - - -Problem Component Code -*************************** - .. code-block:: xml -

The dopamine molecule, as shown, cannot make ionic bonds. Edit the dopamine molecule so it can make ionic bonds.

-

When you are ready, click Check. If you need to start over, click Reset.

- - - - - +

+ A molecular structure problem lets the user use the JSME editor + component to draw a new molecule or update an existing drawing and then + submit their work. Answers are specified as SMILES strings. +

+

+ I was trying to draw my favorite molecule, caffeine. Unfortunately, + I'm not a very good biochemist. Can you correct my molecule? +

+ + + + + CN2Cc1[nH]cnc1N(C)C2=O + JME 2014-06-28 Wed Jul 23 13:41:18 GMT-400 2014 + + 12 13 0 0 0 0 0 0 0 0999 V2000 + 3.6373 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6373 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4249 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2124 3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2124 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4249 1.4000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9688 1.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7917 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9688 3.9326 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 1.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4249 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 1 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 2 9 1 0 0 0 0 + 1 7 1 0 0 0 0 + 5 10 2 0 0 0 0 + 4 11 1 0 0 0 0 + 6 12 1 0 0 0 0 + M END + + + Cn1cnc2c1c(=O)n(C)c(=O)n2C + + + C8H10N4O2 + - +
+

Explanation

+

+ Some scholars have hypothesized that the renaissance was made + possible by the introduction of coffee to Italy. Likewise scholars + have linked the Enlightenment with the rise of coffee houses in + England. +

+
- -**Problem 2** - -:: - - -

The dopamine molecule, as shown, cannot make strong hydrogen bonds. Edit the dopamine molecule so that it can make strong hydrogen bonds.

- - - - - - - -**Problem 3** - -:: - - -

The dopamine molecule has an intermediate hydrophobicity. Edit the dopamine molecule so that it is more hydrophobic.

- - - - - - \ No newline at end of file diff --git a/docs/en_us/course_authors/source/exercises_tools/molecule_viewer.rst b/docs/en_us/course_authors/source/exercises_tools/molecule_viewer.rst new file mode 100644 index 0000000000..1774fe3821 --- /dev/null +++ b/docs/en_us/course_authors/source/exercises_tools/molecule_viewer.rst @@ -0,0 +1,98 @@ +.. _Molecule Viewer: + +####################### +Molecule Viewer Tool +####################### + +Studio offers two tools that you can use in discussions of molecules: + +* With the **molecule viewer** tool, you can create three-dimensional representations of molecules for students to view. +* With the **molecule editor** problem type, you can allow students to draw their own molecules. For more information about this tool, see :ref:`Molecule Editor`. + +Both tools use **JSmol**, a JavaScript-based molecular viewer from Jmol. (You don't need to download this tool; Studio uses it automatically.) For more information about JSmol, see `JSmol `_. + +The following image shows the molecule viewer tool in a course: + +.. image:: /Images/MoleculeViewer.png + :width: 500 + :alt: Image of molecule viewer showing a molecule of Ciprofloxacin + + + +.. note:: To create a molecule viewer tool, you must have permission to upload files to a third-party file hosting site such as Amazon Web Services Simple Storage Service (AWS S3). When you create the molecule viewer, you'll upload a folder that contains a large number of files to the file hosting site. + +.. _Create the Molecule Viewer: + +******************************* +Create the Molecule Viewer Tool +******************************* + +Creating a molecule viewer tool has several steps: + +#. Download files from the `BioTopics website `_ and from edX. +#. Move or edit some of the files that you downloaded. +#. Upload a folder that contains all of the files that you downloaded and edited to your own file hosting site. +#. Create an HTML component that contains an IFrame in Studio. The IFrame references the files that you upload to the file hosting site. + +================================================ +Download Files from BioTopics and edX +================================================ + +#. Create or download a .mol file for the molecule that you want to show. You can download a variety of .mol files from the `BioTopics website `_. Save the file in a place where you can easily find it. +#. Download the `MoleculeViewerFiles.zip `_ file from edX. +#. Unzip the `MoleculeViewerFiles.zip `_ file that you've downloaded. + + When you unzip the file, you'll see a **MoleculeViewerFiles** folder that contains the following folders and files: + + * data (folder) + * j2s (folder) + * js (folder) + * MoleculeViewer.html (file) + +================================================================ +Move the .mol File and Edit the MoleculeViewer.html File +================================================================ + +#. Move the .mol file that you downloaded from BioTopics into the **data** folder that you downloaded from edX. +#. Edit the MoleculeViewer.html file: + + #. In a text editor, open the MoleculeViewer.html file. + #. In line 19 of the MoleculeViewer.html file, change **Example.mol** to the name of your .mol file. For example, if you downloaded the Glucose.mol file, line 19 in your file will look like the following: + + ``script: "set antialiasDisplay; background black; load data/Glucose.mol;"`` + +3. Save the MoleculeViewer.html file. + +================================ +Upload Files to a Hosting Site +================================ + +#. Make sure that your **MoleculeViewerFiles** folder contains the following folders and files: + + * data (folder): Earlier, you added a .mol file to this folder. + * j2s (folder) + * js (folder) + * MoleculeViewer.html (file): Earlier, you changed line 19 in this file. + +2. Upload the entire **MoleculeViewerFiles** folder to your file hosting site. + + .. note:: Because this folder contains many files, uploading the folder may take several minutes, even over a fast connection. + +=============================== +Create a Component in Studio +=============================== + +#. In Studio, open the unit where you want to add the molecule viewer. +#. Under **Add New Component**, click **HTML**, and then click **IFrame**. +#. In the component editor that opens, replace the existing content with your own text. +#. In the toolbar, click **HTML**. +#. In the **HTML Source Code** box, enter the following line in the place where you want the molecule viewer to appear: + + ``

`` + +6. Replace ``path_to_file`` with the URL of your file hosting site. For example, the line may look like the following: + + ``

`` + +7. Click **OK** to close the **HTML Source Code** box, and then click **Save** to save the component. +#. Click **Preview** to see your component as a student would see it. \ No newline at end of file