Web MOIL example:
    Solvation of the Arc Repressor protein dimer from its PDB file

This example shows the step by step operations of how to submit a MOIL job to the CBSU cluster at Cornell University with MOIL build-in web client. (a desktop version of this example was prepared by Alfredo Cardenas)

  1. Use MOIL to read PDB file (1PAR.pdb), extract the sequence information (poly file), compute the connectivity information (wcon file), and convert the coordinates from PDB format to moil coordinate file (CRD);
  2. Solvating the protein in a box of water molecules.

Now, we accomplish this task through the MOIL web interface for the Windows platform. The following steps show how to submit job, to check status of the submitted job, and to use MOIL molecular viewer to display the final structure.


Screen ShotStep Description
I. Send job request

1. Start MOIL Graphic User Interface (moil.tcl);
2. From the main menu, click Assemble->"Process PDB";
3. Worksheet pops up;
4. Use file browser to fill in the PDB file name (user can type in the name as well);
5. Double click to select the file 1PAR.pdb;
6. Unclick "Use Default Parameters" to expand worksheet;
7. Worksheet expands;
8. Fill in Water Box size(50x50x50) and click "Run on Web" button to submit job to the CBSU web server.

The default maximum CPU time is 60 minutes. You can change it through "System->Set Max Batch Minutes" before issuing the "Run on Web" command.
9. Fill in your email address to receive a notice from the CBSU server when your job is completed, click "Submit Job" to send the job request to the CBSU through the Internet; (If "Close" is clicked, the job request will not be send.)
10. Wait for the Web response;
II. Check job status

11. The web response is saved in your currrent working directory as *_sub.html for later job check/delete.
12. Open the saved web response html file;
13. Click the link for job status;
III. Get job result

14. Check your email for a link to your results, download and unpack the results;
IV. View structure

15. Click from the main menu "View Structure"->"New Config File" to view the structure;
16. Cmoil worksheet pops out. Fill in the *.wcon and *.crd file name, and set the file type to CRD;;
17. Click "View Structure", and the structure graph pops out.