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Molecular Graphics Project Information

Molecular Graphics Project .pdf (for those who wish to have a hard copy of the Fall 09 instructions!).

Bioc 463A Molecular Graphics Project

Important Dates and Deadlines:

• Jan. 25, 26, 27: Workshop in BSW 243 (computer lab) from 6 pm to 8 pm: Workshops for initial instruction on Jmol and developing a Jmol webpage:   The same material will be covered in each of these workshops, so only attend one due to limited seating.  A sign up sheet will be provided in class.
• By Feb. 16: meet with or contact Dr. H about the protein that will be subject of your group's Jmol webpage.
• By Mar. 9: meet with Dr. H to show progress on Jmol script development.
• Mar. 29: all Jmol webpages, scripts, and jpegs must be submitted to Dr. H.
• Apr. 2: Jmol gallery will be created on course website.
• Apr. 23: submit grades for class mates Jmol webpages to Dr. H as a group.

As you can see, you will need to begin working on this project right away, do not put it off!

Introduction:
An incredibly useful tool in molecular sciences is the ability to visualize molecular structure by a variety of different means.  This is why you were encouraged to buy and actually use modeling kits in Organic Chemistry.  Those who actually used their modeling kits found that they understood concepts such as stereochemistry, steric interference or overlap, and symmetry much better than their peers who thought such advice was unnecessary.  In biochemistry, an understanding of protein structure is virtually impossible if you can not visualize the protein structures, which is why there has been so much effort in developing user friendly molecular graphics programs, most of which are freely available on the Internet. Biochemists often use images generated by molecular graphics programs to aid and enhance their interpretation and description of their experimental results. Being molecular graphics “illiterate” is no longer an option in modern biochemistry.

In order to either introduce you to, or enhance your knowledge of, molecular graphics programs we have developed this Project using a widely used visualization program called Jmol.  There are several other programs that are widely used by researchers: Deep View, PyMol, MolMol, Insight II, etc.  Each one of these programs has its advantages and disadvantages.  PyMol, for instance is often used to produce some very high definition and beautiful jpeg files for publication, however the developers of this program intentionally have invested their efforts in developing applications and routines rather than making the program user-friendly.  Jmol was developed to both be beneficial to the novice to medium user and has been widely adopted by such entities as The Protein Data Base (RCSB) and the newly emerging website Proteopedia. Jmol evolved from a molecular graphics program called RasMol (raster molecular graphics), that was developed by Eric Martz at University of Massachusetts, Amherst in the early to mid 1990’s.  RasMol was widely used by educators throughout the mid to late 1990’s to develop Chime routines that could be utilized in the classroom.  Chime, while a very useful educational tool was very cumbersome to use.  Almost all of the Jmol routines used in Bioc 462A were originally written as Chime routines by the late Professor Michael A. Wells in the mid to late 1990's and then converted over to the Jmol format in 2004. Both Chime and RasMol are no longer supported and have been largely abandoned.

Jmol utilizes many RasMol algorithms for their program and command structure.  In order to fully understand how to use Jmol, it is still necessary to understand RasMol command line scripting, paying particular attention to the command line syntax, especially when developing Jmol scripts.  The developers of Jmol also attempted to to make many of the RasMol functions “point and clickable”, a substantial improvement over the extremely limited number of things you could do in RasMol using your mouse.  There have been other extensive improvements made by the Jmol developers, most recently the ability to produce molecular surfaces often used to show the topology of the protein surface in a much better way than can be accomplished with solid surface or CPK rendering of individual atoms. 

Overview of Project:

• Work in group of three or four.
• Choose a protein which we will study in Bioc 463A from the Protein Subject for Jmol Pages listed below for which you will develop a Jmol page.
• Develop a Jmol page displaying the protein in a minimum of two views.
• Description of protein will be: (1) a general or overall picture of the structure of the protein and how that structure is related to the in vivo function of the protein, then (2) at least one other image related to the experiment we actually performed in class and how that protein's structure is related to the data or results that were obtained.
• These descriptions will require you to do substantial outside research on the protein you choose.
• The Jmol web pages will be posted on the 463A website in the Molecular Graphics Gallery so the entire class can view, critique, and grade them.
• There will be deadlines (see below) for various aspects of the project.  Each group must meet with Dr. Hazzard by these deadlines to show him their progress.

Learning How to Use Jmol:

   In order to get everyone started on Jmol, there will be three introductory workshops (see schedule above) held in the Computer lab (BSW 243). During this workshop we will give a brief history of molecular visualization, introduce you to some incredibly useful websites listed below, and give you a brief and simple project to work on. It then becomes the responsibility of the students to learn how to use Jmol and ultimately develop the web pages.

Workshop information: Jmol_Workshop.pdf

What will be provided:

We will post on the course website a generic Jmol routine folder (borrowed from Bioc 462A) that will contain the “html” web page, the “.txt” file containing the commands (aka scripts) for the displaying the Jmol image, and the “jpegs” files that are used as an aid to see what the image should look like.  It will be necessary for you to have access to a web page editing program and know how to use it.   The Bioc 462A website has a large number of Jmol routines that can also be examined to get ideas about formatting your page.  The OnLine Macromolecular Museum (OMM) also has instructions on generating an html page and extensive documentation of the scripts used to develop their pages.  You will also be given instructions for downloading Jmol onto your own computer which is very helpful, although not absolutely necessary, for developing your scripts and any jpeg file you might want to output to include on the final html page.

Protein Subjects for Jmol Pages

Useful Websites:
Each one of the following websites has its own designated emphasis and utility.  It is up to everyone to become familiar with the unique attributes of each of them.  We will touch briefly on each on during the workshop.

Protein Data Base: www.rcsb.org (when downloading files for Jmol pages, use the "*.pdb.gz" format, the coordinates will load faster". For being able to read the file, download the "*.pdb" format).

Bioc 462 Jmol routines: http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/routines/routines.html

Jmol: www.jmol.org

Jmol interactive scripting: http://jmol.sourceforge.net/demo/#Interactive%20applet%20demonstration%20pages

RasMol: http://www.umass.edu/microbio/rasmol/

RasMol Commands: http://www.umass.edu/microbio/rasmol/distrib/rasman.htm (good listing of all commands, poor on syntax help)

RasMol Select/Restrict tutorial (extremely useful): http://www.umass.edu/microbio/rasmol/seleccmd.htm

OnLine Molecular Museum : http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/gallery.htm (an extremely well done website with tutorials on scripting and many really cool Jmol routines)

Proteopedia (a wiki site for protein structures): www.proteopedia.org (you can generate your own Proteopedia page on a protein of interest once you have joined).

Jmol webpage development related material:

For all work with any web site using molecular graphics DO NOT USE INTERNET EXPLORER!!!! Firefox works very well. Mac users, you are on your own!!

The following are the "how to" files written by Daniel Martinez for virtually everything we could think that you might have problems with:

When downloading the Protein Data Base (PDB) file for developing your Jmol scripts, always work with the "zipped" version ("*.pdb.gz"), it will load much faster than the ASCII version ("*.pdb") which is better for "reading"!

When submitting your final version, DO NOT include the entire Jmol operating system, we already have that information. Only submit your scripts, jpegs, and html page.

jmol_howto_dwnld.pdf: an explanation how to download and install jmol on your own computer.

MolGraph_folder.zip: downloadable folder containing pdb, *.txt, and jpeg files.

jmol_setup.pdf: setting up and using your MolGraph_folder files.

using_jmoljar.pdf: a "how to" manual for working with and within the jmol.jar editing window.

jmol_html.pdf: a printable version of the html template and an explanation of what needs to be changed in your final html page.

• A total of 30 points will be possible for this project: 15 pts from your peers and 15 points from the GTA's.
• Each section will only grade Jmol pages for other groups in your section.
• Grades for other groups will be submitted as a consensus score for your entire group.
• The grade will be worth a total of 15 points, equally distributed between the three topics listed below.  Turn in the score for each topic.
• Any  grades of 2 or less per topic must be accompanied with a written justification.
• Submit grades to Dr. H. by Dec. 6 AS A GROUP for the Jmol pages in your section.

Topical breakdown for grading:

• (5 points maximum) Written content: How well is the textual material written?  How thorough is the story being told about the protein?  How well does the text explain the experiment that was performed in class?
• (5 points maximum) Connectivity:  How well is the text connected to image being displayed?  Does the image clearly accentuate the story being told in the text?
• (5 points maximum) Artistry: This is where the “Wow” factor comes into play.  Is the image clear and to the point or is it very busy with superfluous and confusing material?  Are there any cool special features such as animations, morphs, etc.? Do the special effects enhance or overwhelm the efficacy in telling the story?

Molecular Graphics Grading Sheet: will be updated once topics have been chosen.