Adding a protein to the system

These directions are for adding a new protein definition file to the Ion Exchange web site. Once a new protein definition file has been added to the web site, you will be able to use the protein in an ion exchange simulation and view the protein's structure using Chime.

In order to complete these steps, you must have write privileges on the server that contains the ion exchange web site. The only tool that is required is a text editor.

To use a new protein in the simulation applet:

  1. Locate the Protein Data Bank (PDB) file for the protein you wish to add to the web site. PDB files may be downloaded from http://www.pdb.bnl.gov.
  2. Copy the PDB file to the directory /root/pdb, where root is the root directory for the ion exchange web pages.
  3. Open the file /root/pdb/pdb.idx using a text editor. This file contains a single line for each protein known to the system. Add a line for the new protein by starting the line with the name of the protein as you would like it to appear, followed by a tab character, followed by the name of the PDB file. Use the existing lines as an example.

To make a new protein viewable using Chime:

  1. Locate the Protein Data Bank (PDB) file for the protein you wish to add to the web site. PDB files may be downloaded from http://www.pdb.bnl.gov.
  2. Copy the PDB file to the directory /root/pdb, where root is the root directory for the ion exchange web pages.
  3. Create a new HTML file in the directory /root/html/ using a text editor. Name the file pdbXXXX.html, where pdbXXXX is the file name of the protein's PDB file. Using an existing pdbXXXX.html file as an example, create the contents of the HTML page. The following two lines will need to be modified:
  4. Edit the file /root/html/molecule.html using a text editor. This file contains links to the HTML pages that embed the Chime plug-in for each of the protein molecules. Add a link to the new HTML page that you created in the previous step. Use the existing links as an example.