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
- 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
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.
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.
(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.
If you are unfamiliar with DNA structure, refer to the following
Last updated 8th Feb '96