email questions/comments to
johno@email.arizona.edu
Here is a Pymol manual (2004 version)! Don't print this out unless you want 66 pages of manual!
October 10, 2007.
By popular demand, the due date for the final papers has been postponed to October 31! I will not actually check for these papers until the morning of Nov 1. Take whatever action you deem necessary.
The due date for the reviews has not changed! The reviews are due on November 7, 2007.
Be sure to follow the instructions for authors:
Figures: The largest dimension of your figure should be 6 inches at 72 pixels per inch = 432 pixels!
October 8, 2007. Bring hard copies of your papers to class on Wednesday the 10th to show to your group!
Here is brief guide to writing a scientific paper from the Biology Department of Lewis and Clark University:
October 5, 2007
Here is a link to a page with a lot of pymol examples:
Note that many of these scripts go beyond what is needed for plain visualization.
Here is another, with scirpts to do relatively simple things:
Here is another:
October 1, 2007
Here is the long-awaited "Instructions For Authors"!
Instructions
For Authors
Cover Art: A special
figure will be selected for the "cover" of the Proceedings. All
figures submitted will be considered. However, contributions of
figures especially for the cover may also be submitted. These
figures must be at least vaguely related to your article. If you
can make a particularly remarkable picture of your protein, submit it
for the cover! (5 pts to the student whose figure is chosen for
cover art.
September 21
Next week: Abstracts due 200-250 words, 3 major references!
Pymol script for cytc:
September 14
Here is the SMase D script:
September 11
A Cement Truck Full of Margaritas....
September 9
Tutorial Section, Sep. 12:
For class on Wednesday, September 12 bring in your ideas for your paper. If you are going to use your senior thesis, bring in a paragraph describing your project and one major paper. If you are not using your senior thesis bring in a paper and/or News and Views article describing a suitable idea. If you are unsure of the suitability of your idea, please talk with Dr. O. See the "call for papers" below.
Review for Exam 1.
Most of the class period on Sep. 12 will be devoted to a review for Exam 1, which is Monday September 17th.
Proceedings of Biochem 362a Honors -- Call for Papers
The Proceedings of Biochem 362a Honors publishes review papers of particular quality in the broadly defined area of biochemical structure and function. Papers submitted to the journal should review a scientific problem in which high resolution protein or DNA structures contribute in a fundamental way to the understanding of the problem. The "Instructions for Authors" will be available soon.
Computer Section Sep. 14
We are going to look at structure/function relationships in Sphingomyelinase D. SMase D is a enzyme from Loxosceles spider venom that causes serious dermatologic lesions. This is an example of the type of structure/function paper on which you could base your reviews. We will go through the paper, look at the figures, compare them with the structures visualized by RasMol and discuss the mechanistic implications. You should download the paper, Murakami et al., Journal Biological Chemistry, 280: 13658-13664 (2005) and read it before class.
September 4, 2007
Updated Rasmol Tips: rasmol_tips_v2.txt
All the commands you will need for your assignment are in the "tips" file. Download it to your directory so you can refer to it as you work.
Your assignment for Friday's class is to write a script that will produce the following picture of cytochrome c. Email the script to Dr. Osterhout. Don't panic. Get help from your group members.
Do not worry about reproducing the exact colors, but please try to make it pretty.
August 30,
2007.
The Rasmol tips file has been updated! See above.
The Rasmol tips file has been updated! See above.
Announcement: Dr. Osterhout will be
attending Venom Week, which is an international meeting concerning
venom and venomous creatures, next week. Dr. Park will be in
charge of the tutorial section and the computer section. Dr. Park will
also take Dr. Osterhout's office hour (Tuesday 11:00-noon).
August 28, 2007.
John Osterhout will hold office hours Tuesdays at 11:00 am - Noon in BSW 347. If no one is in BSW 347, come around the corner to my office, BSW 345, and get me!
August 10, 2007.
Welcome to the honors section of Bioc 462a! The honors tutorial and the associated computer section are designed to augment your Bioc 462a experience. Activities include problem solving, an introduction to the scientific literature, literature searching, use of the Protein Data Bank, molecular visualization, manuscript preparation, evaluation of scientific ideas and the preparation of scientific presentation materials such as graphs and slides.
Bioc 462a Honors consists of two parts:
Tutorial Section: Part of the tutorial section will be devoted to problem solving. We will concentrate on problems related to the course material but "enhanced" in ways to increase understanding. We will practice estimating the answers to scientific problems and will also work on problems for which there are no exact solutions. These are intended to enhance your effectiveness on the exams and in the real world. Part of the tutorial section will be devoted to writing a review paper which will be submitted for on-line publication in the "Proceedings of Bioc 462a Honors" . You will be coached in the choice of topics for review, in the preparation of graphs and figures and in manuscript preparation. You will also be expected to participate in the review of articles submitted for publication.
Computer Section: In the computer section you will practice computer skills that will help you understand structure-function relationships and prepare your article for submission to the class journal. These skills include: literature searching, the Protein Data Bank, molecular visualization and the preparation of scientific graphs and figures.
Biochemistry
462a
Department of Biochemistry and Molecular Biophysics
The University of Arizona
johno@email.arizona.edu
All contents copyright © 1998-2007. All rights reserved.
Last revision fall 2007
Department of Biochemistry and Molecular Biophysics
The University of Arizona
johno@email.arizona.edu
All contents copyright © 1998-2007. All rights reserved.
Last revision fall 2007