The text presented in this web page was written up using Microsoft Word, then copied and pasted into an html document. The protein images (Penicillinase, D-alanyl-D-alanine Carboxypeptidase) were obtained over the internet from the protein databanks Brookhaven Protein Database and Molecules R US (as pdb files). These databanks give the coordinate values (X, Y, Z) of each atom in the protein. These coordinate values, in turn, were translated into three dimensional images using Rasmol. The Penicillin and D-alanyl-D-alanine images were created using Spartan and MacSpartan. Both the Rasmol and Spartan images were then cut and pasted into GraphicConverter for labelling, then saved as GIF files (also with GraphicConverter).
The Rasmol program permits manipulation of images at the molecular level. Each amino acid residue in the protein is sequentially numbered from N-terminus to C-terminus and may be selected then sized, colored, grouped, or removed individually. Some of the pdb files also contain coordinates for hetero molecules, like water or substrates, which are not part of the actual protein, but serve to show binding/catalytic sites as well as crystal structure.
The images were saved into the folder with the web page html document and were inserted into the page using Netscape Navigator Gold. The web page was brought up and the Edit icon was clicked on. This results in a message saying that in order to be edited the page must be saved locally; saving it to the same file that created it (replacing the web page html document with it) ensures that the same web address will bring up the newly edited file and all the changes made wont be lost in transition from local to global. By merely clicking on the icon labelled Insert Image a menu appears, since the image files were in the same folder we could select the choose file option which automatically brings up a list of the other files in the folder. There are also icons to align the picture on the left or right side of the page and to wrap text around it or not.
Most of the sources of information used for creating this page have been linked to:
The one book we used was:
Voet, Donald and Judith, Voet. Biochemistry John Wiley & Sons inc. New York 1995