WebMO Program Help

Getting Started

The WebMO computational chemistry package facilitates computational chemistry on the WWW. WebMO permits the access of various computational chemistry packages over the WWW using only a web browser. Computational chemistry jobs can be created, queued, run, viewed, downloaded, and deleted without the hassle of a UNIX shell. It is even possible to import existing jobs to be viewed within the context of the WebMO interface.

Job Manager

The job manager is where all WebMO jobs are managed. In the job manager, jobs are created, viewed, downloaded, killed and deleted.The job manager displays a list of completed jobs, failed jobs, as well jobs that are queued and those that are currently running. The list of jobs can be filtered by selecting the appropriate filters, and clicking the filter button located at the head of the job list.

Completed jobs can be viewed by clicking the View button next to the corresponding job. Likewise, the raw output from a failed job can be viewed by clicking the "Raw Output" button next to the job.Queued or running jobs can be aborted or removed from the queue by clicking the "Kill" button next to the corresponding job.

Outdated jobs can be deleted by first selecting the checkbox next to the job(s), and then clicking the "Delete" button at the bottom of the page. Similarly, jobs can be downloaded by first selecting the checkbox next to the job(s), and then clicking the "Download" button at the bottom of the page. A spreadsheet summary of jobs can be created by selecting the desired jobs and clicking the "Spreadsheet" button at the bottom of the page (WebMO Pro only).

To create a new job, click the "Create New Job" button; to import and existing job, click the "Import Job" button. The new job will appear at the end of the jobs list as either queued or running.

Creating and Running Jobs

Building a Molecule

After clicking "Create New Job" in the job manager, you will be brought to the Build Molecule page. This is where you will construct the molecule on which calculations will be carried out. To open the WebMO editor, simply click the "Open Editor" button; use the editor to build the desired molecule, and then close the editor.

Import an Existing Molecule

Alternatively, you may import an existing molecule from an existing file in a variety of formats (MOL, PDB, XYZ, Gaussian style, Mopac style). Simply click the 'Import Molecule' button, select the file format and file name (or paste the contents into the provided text box). To automatically generate bonds between atoms, select the 'Generate Bonds' checkbox. Click the 'Import' button to finish the import process.

When the molecule is complete, click the right arrow at the bottom of the page to move to the next step.

Choose Computational Engine

Next, you will be brought to the Choose Computational Engine page. This is where you will choose the computational package which will be used to run calculations on the specified molecule. Select the desired computational package from the list, and click on the right arrow to move to the next step.

Select Job Options

Finally, you will be brought to the Job Options page. The specific options on this page will be unique to each computational package, but will include the type of job to run, theory, basis, etc. When the desired options have been set, click the right arrow to submit the job. You will now be returned to the job manager. You should see your new job listed at the bottom of the jobs list, either running or queued.

Viewing Results

Introduction

Jobs can be viewed by clicking the "View" button next to any successfully completed job listed in the job manager. You will then be brought to the View Job page, which contains the WebMO viewer, as well as a list of calculated molecular properties. The WebMO viewer contains the final optimized molecular geometry, which can be explored using the same techniques as in the editor.

Viewing Calculated Properties

Several molecular properties contain an associated "View" button. Clicking this button causes the corresponding property to display on the WebMO editor. All displayed properties can be removed from the viewer by clicking the "Reset Viewer" button. In addition, the raw output of a job can be examined by clicking the "Raw Output" button.

Starting Another Calculation

To create a new job using the optimized geometry currently displayed in the WebMO viewer, simply click the "New Job Using This Geometry" button. You will then be brought to the Build Molecule page, where the geometry can be tweaked as necessary.

Exporting a Molecule

The optimized molecular geometry can be exported in a variety of formats using the 'Export Molecule' button. Simply select the desired file format, and click the 'Export' button. You may save the resulting text file using your browsers save capabilities. To view the molecule in an external viewer (i.e., CHIME), click the 'Open in External Viewer' checkbox.

Importing an Existing Job

After clicking "Import Job" in the job manager, you will be brought to the Import Job page.

  • To import an existing output file residing on the server, enter a job name, the computational engine used to run the job, and the absolute system path to the job.
  • To import an existing output file residing on the client, enter a job name, the computational engine used to run the job, and click the "Browse" button to select the desired output file.
  • To add a previously downloaded WebMO archive back to the Job Manager, click the "Browse" button to select the desired WebMO archive (*.tar)
Once you have entered the required information simply click the "Import Job" button to execute the import. A status message will notify you of any errors encountered during the import process. To return to the job manager, click the "Return to Job Manager" button.

Managing Jobs

Jobs listed in the Job Manager can be organized into a system of folders. Two folder, the Inbox and the Trash, are special; all newly submitted jobs appear in the Inbox, while deleted jobs are temporarily stored in the Trash.

  • To move to a different folder, select the destination folder from the folder list and click Move.
  • To move a job to a different folder, select the job(s) by checking the check box to the left of the job, select the destination folder from the folder list and click the Move button.
  • To delete a job, select the job(s) and click the Delete button. This will automatically move the job to the Trash folder. If the job is already in the Trash folder, this will permanently delete the job.
  • To download a job, select the job(s) and click the Download button. This will create an archive containing all output related to the job and that is automatically downloaded to your computer.
Additional folders can be created, renamed and deleted by clicking the Folders button (WebMO Pro only).
  • To create a new folder, type the new folder name in the text box and click the Create button.
  • To rename a folder, select the target folder, type the new name in the text box, and click the Rename button.
  • To delete a folder, select the target folder and click the Delete button.

Editing your user profile

After clicking "Edit Profile" in the job manager, you will be brought to the Edit User page. To change your password, enter your current password, new password, confirmation, and then click the "Submit" button directly below the confirmation.

To change your e-mail address, and e-mail notification, make the appropriate changes and click the submit button. E-mail notification will send out an e-mail to the specified address when a WebMO job is complete.

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