Assignments
General notes regarding assignments:
- Each student is allowed 2 late days to use during the quarter when submitting the assignments and/or final project. You can use them one at a time, or all at once, but once they are gone, further late assignments will be penalized (-10% per day).
- The assignments will be based on many resources available on the web. It is very important that web pages, servers, research papers, textbooks, etc. used for assignments and the final project are cited properly in a reference section. I will not tolerate plagiarism of any kind.
- Assignments are given in DOC or PDF format. In return, you have the choice of format to hand out your documents:
- Paper copy is fine; you can give it to me at the end of the lecture, or in my homework box, as soon as I figure out where it is!
- A web page containing all the results (preferred). Many Word processing programs can generate html files. If you want to program HTML yourself, there are many HTML primers on the Web. Have a look at: BareBones Guide to HTML
Send me the URL where I can view the page, or send me an archive with the html file and all attached images... - A Word file or a PDF file is fine. Send them to me by e-mail
- My e-mail address is: koehl@cs.ucdavis.edu
| Assignment | Title | Handouts | Due | Notes |
| 1 | Protein Structure Vizualisation: Using Pymol | Word File PDF file |
October 30, 2007 | |
| 2 | Protein Geometry | Word File PDF file Test file for atom coordinates and radii: Test.crd |
November 25, 2007 |
The file Test.crd is organized as follows:
- line 1: number of atoms (M)- line 2 to M+1: for each atom, provide X, Y, Z and R |
| 3 | Protein Structure Modeling | Word File PDF file Test files :
(Ref. energy file: Model1.ene) |
December 13, 2007 |