Design Guidelines for Macromoleculr Structure Presentations
in Protein Explorer (PiPEs)

by Eric Martz for Protein Explorer. (Original 1998, revised 1999, 2001, 2005).

Note 1: These guidelines were originally written for students in a class that I taught. Therefore, some points below may be familiar to non-students, or are inapplicable.

Note 2: In some cases, it is unnecessary to spend the time to save command scripts and install them in a PiPE, because Protein Explorer makes it easy enough to show the desired views with its generic exploration buttons and menus.

"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 may plan to illustrate with your web presentation.


  1. Choosing your presentation topic. Your topic can be a single molecule, a group of related molecules, or a principle illustrated in a number of molecules.
    1. Investigate what is already available on your topic on the web, especially as interactive (rotatable) molecular structure visualization. The best place to start is the World Index of Biomolecular Visualization Resources ( You can also search the web for your topic and "chime" (and maybe "pdb").
        (There is no mechanism known to me to search for websites that invoke Chime, since the invocation is by MIME type in an <embed ... > tag, and I know of no way to search for e.g. ".pdb" or ".spt" within an embed tag. Unless the author happens to mention "Chime" in the text, the word "Chime" may not occur in the website.)
    2. If you find your topic already presented in Chime on the web, this does not mean you can't do that topic. You need to evaluate what is on the web. You could decide to do a better job, or to do an aspect of the topic not covered in what is already available. It does mean that you should give careful thought to your plan, and discuss it with others involved. If you stick with this topic, you must cite and link any related resources you find.
    3. Make sure that suitable PDB file(s) are available! There are no reliable atomic coordinate data for many excellent topics!
    4. You may find excellent non-interactive resources on your topic -- text only, or with static images. Save the URL's, and if appropriate later link them into your presentation.

  2. Limited time for your talk? If the scheduled time for your talk is brief, you need not show all parts of your web presentation in your talk.

  3. 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. The main point(s) to be taken from each image must be clearly stated. 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 in HIV Reverse Transcriptase, part of his On-Line Macromolecular Museum (California Lutheran University, Thousand Oaks). This is great if you have the time and inclination but is not necessary in order to make a widely useful web presentation.

  4. In most cases, linked words or phrases should describe the resource being linked. This design recommendation is generally desirable for all websites. Examples:
    Good design:
    For reference documents on commands for Protein Explorer (PE), see Using Commands.
    Using Commands provides links to explanations of all commands.
    Poor design:
    For reference documents on commands for Protein Explorer (PE), click here.

  5. All sources must be cited. Citations to journal articles of major importance to your presentation (those listed at the bottom of the first page) should be complete (including authors, year, title, journal volume and page). Your bibliography should be annotated with short notes telling what is particularly noteworthy or useful about each article. Journal references should be linked to PubMed ( Search at PubMed and when you find the paper, copy the URL and paste it into a link, for example Martz, 2002. PDB filenames can be linked to the Protein Data Bank by substituting their 4 character code at the end of, for example 1d66.pdb. You may prefer also to cite the original papers for PDB files featured in your web presentation, e.g. 1d66.pdb ( Marmorstein et al., 1992), although the original paper is linked to the PDB record. Books should be cited fully and hyperlinked to the publishers page for the book if you can find it.

  6. 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 in fall [year]."

  7. You must have permission to include copyrighted images or other content taken from a website or scanned from a publication. Usually this is as simple as emailing the copyright holder and asking for permission. Don't put it off -- ask as soon as you think you may use materials from another website. Waiting till the end of the semester is problematic.

  8. Most Chime buttons should be independent. That is, each button should generate the same image regardless of which button was pressed immediately before. This enables you to skip some buttons, or to back up to answer a question, without producing unintended or corrupted molecular views.

    The simplest way to accomplish this is to use scripts saved from Protein Explorer's Recorder. These always start by resetting the molecular orientation and size. (An older technology that also works is to use scripts saved from RasMol or Chime. These always load the molecule at the outset, guaranteeing a uniform result.)

    In some cases, it may be preferable to have a few buttons that 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: &nbsp; &nbsp;. There are examples for Antibody: click on Immunoglobulin Domain).

  9. All color schemes should be explained with color-matched text. Examples:
    Good design:
    Nucleotides are A T G C.
    Bad design:
    A is blue, T is yellow, G is green, and C is red.
    Horrible design:
    A is blue, T is yellow, G is green, and C is red.

  10. Use colors that stand out against the background: avoid blue on black! The most common error is to use pure blue (RGB hex 0000FF) on black. Chime (or rarely, Protein Explorer) may assign blue to one chain. If this happens and you are using a black background, it is your responsibility to select this chain and color it with a lighter color (e.g. 8080FF as above)! While blue may look OK on black on your screen, it is usually very dim or invisible when projected.

  11. Use standard color schemes when available. Standard color schemes include those in Protein Explorer's QuickViews COLOR menu (Element, N->C Rainbow, Structure, Temperature, Polarity2,3,5, ATGCU, etc.). The complete set of standard color schemes is DRuMS. If you use a nonstandard color scheme, there should be a compelling reason.

  12. All PDB files greater than a few kilobytes in size should be gzipped. See Gzipping PDB files for Chime at the UMass Chime site FAQ.

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 that is uneven in quality, incomplete and not well designed because you ran out of time.

  2. The PiPE Template is strongly recommended. It comes with detailed instructions, and provides a good basic design for most molecular structure presentations. Experience has taught me that devoting at least 1/3 of the screen to buttons/text is 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. The molecule always spins slowly to enable the audience to see its three-dimensional qualities at all times. (The speaker can stop the spinning easily, but this is not recommended because it is easy to forget to re-start spinning, and then the 3D structure "dies" for the audience!) Unanticipated questions can be answered during a talk by using QuickViews or other capabilities of Protein Explorer, since PiPE permits seamless transitions between the presentation and PE's tools.

    You may elect to use a different template if you have compelling reasons. In tutorials we are developing, we wanted to show three to six molecules at once, which is not supported by PiPE. Therefore we are developing an alternative, jmol-based template. A jmol-based template has been developed by Craig Martin for his Biomolecular Structure course. 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. Avoid animating 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. A simple example is a zoom to carbohydrate within antibody (click on "Whole IgG1, carbohydrate").

    Although Protein Explorer has a Busy/Ready indicator, people tend to click on other buttons if the movie includes delays due to web transfer, possibly getting frustrated by long animations. Another issue is that people pay more attention and learn better 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 may "fall asleep".

    The move command generates smooth rotations or zooms in a specified number of seconds with a one-line command. It is documented in MDL's Chime command reference manual.

Checklist of the above topics:

  1. Molecule not in Chime on the web already?
  2. Talk not more than ten minutes?
  3. Main point of each image clearly stated?
  4. Links describe resource (not "click here")?
  5. Sources cited and hyperlinked?
  6. Contributors acknowledged?
  7. Permission obtained to include any items authored by others? (Does not apply to hyperlinks.)
  8. All (or most) buttons independent?
  9. All color schemes keyed with color-matched text?
  10. No blue on black!!
  11. Color schemes standard? (DRuMS!)
  12. All PDB files gzipped?


  13. Short and simple?
  14. Use template provided.
  15. Long movie sequences avoided or justified?