Experimenting in Chemistry with Avisto
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| A. Creating 3D Molecular Structures | Movie Demo |
| There are three different ways that you can create a 3D molecular structure. One is to use MolLib for commonly known molecules. Others are to use MolDesign to build it from scratch or edit that from MolLib or MarvinSketch to draw it then convert to 3D structure. Watch the movie demo then repeat the three examples below. |
| 1. MolLib | 2. MolDesign | 3. MarvinSketch |
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1. Double-click on the MolLib button in My Toolbox. 2. On the Rings tab, select the third button on the first row, then click on the 'Send to Workbench' button. 3. You should see the molecular data named 'cyclobutadiene' on the top left of your workbench. 4. If you want to edit it, double click on the molecular data icon will open it in MolDesign for editing. Close MolDesign when it is done, the molecular data will be automatically updated. |
1. Double-click on the MolDesign button in My Toolbox. 2. Select the carbon atom in the Periodic Table with a double bond configuration (sp2). 3. Click on the double half-bond, then click on the carbon atom to select the same bond configuration again. 4. Right click to select 'Add hydrogen', this will create H2C=CH2. Give it a name 'Ethylene' 5. Under File menu, select 'Send to Workbench'. |
1. Double-click on the MarvinSketch button in My Toolbox. 2. Select the benzene button (fifth one on the bottom row) then click on the canvas. 3. Click on the 'Convert to 3D' button, then 'Send to Workbench' button. |
| B. Running applications in Avisto | Movie Demo |
| There are standalone and workflow enabled applications. Watch the movie demo then work through the three examples below using data you just generated. |
| 1. Standalone tools | 2. Simple workflow | 3. Automated multiple application workflow |
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1. Drag & drop Basic QChem Edu tool onto your workbench. 2. Drag & drop cyclobutadiene onto this tool. Basic Qchem Edu will automatically open with the input structure shown on the top right graphic pannel. 3. Use the default runtype of finding 'Stable structure, click on the 'Submit' button. This will submit your job to Astonis cloud computing facility. Once the job is completed, the result structure will be displayed in the bottom right graphic pannel. 4. Right click on the bottom right graphic pannel to send the result to the workbench for storage or view the results in PsiViewer tool. |
1. Drag & Drop the Basic QChem tool (You need to purchase CPU time for this tool, a minimum of two hours is recommended for a semester course) onto your workbench. 2. Move the ethylene molecular data to the front left of it (the cursor position should be on the top left quarter of the tile you want to move the icon to). An green arrow will automatically appear indicating that it is now an executable workflow. 3. Double click on the Basic Qchem Tool to setup running parameter for the job. Use the default runtype in this case. 4. Double click on the green arrow to execute the workflow. Once completed, the resulted molecular data will be placed at the end of the workflow. 5. Double click on the resulted molecular data to view the data in PsiViewer. |
1. Drag & drop both MMEngine and Basic Qchem tools and two folders onto your workbench. 2. Tile these into the workflow as shown below. 3. Double click underneat the folders to label them. Open each application GUI to setup the running parameters. Use the default settings in this case. 4. Drag & drop the ethylene and benzene molecular data onto the folder at the beginning of the workflow, i.e. one with the green arrow. 5. Double click on the green arrow. Once done, on top of the output folder, there will be a number 2/2, i.e. two results have arrived from the two expected number of data. 6. Double click on the output folder and double click on any of the data to view it in PsiViewer. |
| C. Sharing your data with others | Moview Demo |
| You can send your data, the entired workflow with input and output, to your friends and collaborators in a single data object. Watch the movie demo then repeat the step to send your data to at least one friend. View Demo |
| 1. Package your data into a desk | 2. Send by email | 3. Received and unpack the data |
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1. Sweep select the workflow you have done on step 3 above. Then right click to select 'Collapse to desk'. This will replace the workflow by a desk icon. Doulbe click underneat the desk to label it. 2. Double Click on the desk will open it in a popup showing the workflow preserving its spatial arrangement. But there is no green arrow indicating that such a workflow is not executable in the desk. 3. Drag & drop the textSS icon from My Toolbox onto the popup of the desk. Double click underneat it to label 'Read Me'. 4. Double click on the icon for Read Me to open it in a simple text editor and then write some note for your friends. 5. Close the popup window. |
1. Right click on the desk to select 'Email to Friend' 2. This will open a simple email text form. 3. Enter email addresses of your friends, one per line. 4. Write the subject and message to your friend. 5. Click 'OK' when done. This will send the data to your friends. |
1. Save the data from the email to disk, your desktop for example. 2. Open Avisto 3. Right click on My Workbench to select 'Import'. This will open the file chooser for select the data you just received. 4. Avisto will import the data and place it in the original desk format. 5. Right click on the desk to select 'Expand Desk'. This will open the desk and place all the contents onto your workbench. The workflow is now executable. 6. Double click on the green arrow will reproduce the work that your friend just did. |
