PPS '96 - Instructions for Week 4

PPS - Week 4- COURSE SECTION 3

Your assignments for this week are:

Install Mage if you have not already done so. If not, your first stop is the PPS Kinemage Page, which has links to archives where you can obtain the software, as well as many kinemage files.
Mage may be considered a complementary utility to Rasmol. Refer to Eric Martz' description (in his Rasmol home page).
If you experience difficulties, mail any queries to the pps96-technical discussion list.
Configure your WWW browser so that Mage is automatically invoked by it when you click on an appropriate link to a kinemage file. The MIME-type is
```
chemical/x-kinemage
```
Refer to the Technology Page for assistance.
If you have not used Mage before, a good kinemage to start with is the first of the set accompanying the Branden & Tooze Introduction to Protein Structure book. These kinemages have been mounted on the Web server of Brookhaven National Laboratories Structural Biology Department, by PPS Consultant Gail Schuman. Get them from here, or click here for the first kinemage.
For the more advanced: If you are already familiar with Mage, you may wish to consider how to produce your own kinemages. This involves the Prekin program- again, refer to the PPS Kinemage Page (Prekin is currently only available for certain types of computer platform).

Note that much of the Course Material for this week (see below) involves interactive molecules, for use with Rasmol.

Course Material

This week, we turn to Section 3 of the course, which deals with Protein Geometry. This section was written by Jon Cooper of Birkbeck College Crystallography Department. Click here for the Section 3 index.

Your Protein Structure

During this week you will each be assigned an example protein structure which you will study during the course. These structures are from the Brookhaven Protein Data Bank. We will give you instructions on how to obtain the appropriate 'PDB' file, and how you can begin to investigate the geometry of the structure. If you are looking at a PDB file for the first time, you will see that the format consists of the co-ordinates of each atom of the molecule, along with a variety of other information at the beginning of the file. Do not be concerned if at this stage you do not understand all of the different types of record in a PDB file.

The Protein Data Bank, Brookhaven National Laboratories, U.S.
The PDB file format - revised

Looking Ahead

(Don't worry if you don't have time for this during this week)

If you have covered the above and are 'twiddling your thumbs', it will be worth considering the cell biology background to the material on Protein Synthesis, which is the next section of the course, if you are unfamiliar with this field. Study the material on ribosomes.

Course/Tutorial on Cell Biology, by Mark Dalton, Cray Research
Cell Biology Chapter of the Biology Hypertextbook developed by Shane Crotty, MIT.

If you are unfamiliar with DNA structure, refer to the following

The Genetic Code, by PPS Consultant Alan Mills
DNA and the Central Dogma of Life by PPS Consultant Vineet Gupta, University of Rochester, Chemistry Department
The Search for DNA (in the Central Dogma Chapter of the Biology Hypertextbook developed by Shane Crotty, MIT.)
This DNA structure 2bna (59Kb) [Bbk|BNL|ExP|Waw|Hal] (The link was orignally to this one 130d (56Kb) [Bbk|BNL|ExP|Waw|Hal], but as Luis Candeias pointed out, this latter structure doesnt only consist of DNA. What is the other component?)
PPS Consultant Henry Brzeski's Rasmol exercise on DNA structure N.B. you need to run RasMenu to perform all the commands described in this tutorial (e.g. 'spin'). John Reissner explains.

Assignments Index

Last updated 8th Feb '96