Design Guidelines for a Publishable Chemical Structure Presentation in Chime

by Eric Martz for Microbiology 797v: Macromolecular Visualization

All presentations which satisfactorily meet the requirements below will be published on the World Wide Web on the class website.

Terminology:
"Web presentation" is used below to mean what you prepare for public viewing on the web.
"Your talk" is used below to mean the talk you give in class, illustrated with your web presentation.

Requirements

  1. Limit your talk to 10 min. You need not show all parts of your web presentation in your talk.

  2. Your web presentation should stand alone. The goal is that when viewed on the web by a person who did not hear your talk, the web presentation should make sense. This means your web presentation will be unsatisfactory if it requires your verbal explanation in order to make sense. This does not mean that you have to explain everything in detail. You may assume that your audience knows basic biochemistry and you may even assume that your audience knows something about your topic if you wish. While the labels on your buttons can be brief if you wish, they should convey information necessary to understand the image. For example, my DNA and Hemoglobin tutorials assume the audience has read a biochemistry text on the relevant molecule. They are designed to illustrate salient 3D structural features but do not provide a complete introduction to the molecule. Other authors have elected to provide a more complete introduction, such as David Marcey at Kenyon College. This is great if you have the time and inclination but is not necessary in order to make a widely useful web presentation.

  3. Linked words or phrases should describe the resource being linked. This design recommendation is generally desirable for all websites. Examples:
    Good design:
    For details on all commands, see the RasMol Reference Manual.
    or
    The RasMol Reference Manual explains all commands in detail.
    Bad design:
    For details on all commands, see the RasMol Reference Manual, which you can get to by clicking here.
    or
    Click here for the RasMol Reference Manual, which provides details on all commands.
    or
    The RasMol Reference Manual provides details on all commands.

  4. All sources must be cited. Journal article citations should be linked to PubMed. Search at www.ncbi.nlm.nih.gov/PubMed/ and when you find the paper, cut the URL and paste it into a link, for example Sayle and Milner-White, 1995. PDB filenames can be linked to the Protein Data Bank by substituting their 4 character code at the end of http://www.pdb.bnl.gov/pdb-bin/opdbshort?lite_pdb=1&id=1d66, for example 1d66.pdb. It would be best also to cite the original papers for PDB files featured in your web presentation, e.g. 1d66.pdb ( Marmorstein et al., 1992). Books should be cited fully and hyperlinked to the publishers page for the book if you can find it. Here are examples.

  5. All contributors must be acknowledged appropriately with links to personal web sites when available. In particular, if preparing a web presentation for a class, acknowledge the class, for example "This presentation was prepared with guidance from professor Eric Martz in his class Macromolecular Visualization, fall 1998."

  6. Most Chime buttons should be independent. That is, each button should generate the same image regardless of which button was pressed immediately before. The simplest way to accomplish this is to use scripts saved by RasMol or Chime. In some cases, it may be preferable to have a few buttons which modify the image made by another button (or buttons), such as showing a disulfide bond. In these cases, there should be some indication that the button is subsidiary to other buttons, such as indentation, or a button label such as "Disulfide bond. Apply this button to any backbone or cartoon image.". (One way to indent a button is to precede it with perhaps two non-breaking space html codes:    . There are examples for Antibody: click on Immunoglobulin Domain).

  7. All color schemes should be explained with color-matched text. If you use a black background in Chime, you should use a black background for your color key (or maybe for your entire button/text frame, which is how the template is provided). Examples:
    Good design:
    Nucleotides are A T G C.
    Bad design:
    A is blue, T is yellow, G is green, and C is red.

  8. Use standard color schemes when available. Standard color schemes include those in RasMol and Chime (Corey-Pauling-Kulten, Group, Structure, Temperature). If you wish to distinguish all 5 bases in DNA or RNA, consider the template scheme cs_atgc.spt: Azure, Tweety-bird, Green, Carmine, pUrple (used in Eric's DNA tutorial). If you use a nonstandard color scheme, there should be a compelling reason.

  9. All PDB files greater than a few kilobytes in size should be gzipped.

Recommended (but not required)

  1. Keep it short and simple. Don't be overly ambitious. Better to do a high-quality job on a limited set of issues than to try for a broader set of issues and end up with web presentation which is uneven in quality, incomplete and not well designed because you ran out of time.

  2. Use the Template provided. The downloadable template comes with detailed instructions, and provides a good basic design for a linear web presentation. The use of about 1/3 of the screen (this ratio is easily customized) for buttons/text is considered necessary to provide adequate control. Font sizes can be changed dynamically to accomodate the number of people viewing the presentation. A table of contents form is provided, as well as links to useful utilities at the bottom of every page. The molecule always rotates slowly (unless the speaker turns off rotation with the menu) to enable the audience to see its three-dimensional qualities at all times.

    You may elect to use a different template, but it would be best to discuss your reasons with the instructor first. Don't attempt to design your own presentation structure from scratch (html, javascript) unless you can afford to spend a lot of time on it!

  3. Don't animate long sequences of movements. Short zoom movements, lasting a few seconds, are often useful to show the relation of the enlarged moiety to the entire structure. An example is a zoom to carbohydrate within antibody (click on "Whole IgG1, carbohydrate").

    One problem with long programmed moves is that Chime has no indicator that it is busy. People tend to click on other buttons if the move is delayed due to web transfer, or includes intentional delays. The other buttons are ignored because Chime is busy and then people get frustrated and leave. Another problem is that people pay more attention if they need to rotate and zoom the molecule with the mouse, interactively. If the web presentation plays like a movie, it looks pretty but people fall asleep.

    The move command is documented in the "Chime 0.99 draft manual" which you will find on the umass chime website near the bottom. Click on "jump to table of contents", then "commands". Here you will find documentation on several features not yet documented on MDL's site (as of October, 1998).