Design Guidelines for Macromoleculr Structure Presentations
in Protein Explorer (PiPEs)
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.
- Choosing your presentation topic. Your topic can be a single molecule,
a group of related molecules, or a principle illustrated in a number
- 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 (molvisindex.org).
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
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.)
- 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
- Make sure that suitable PDB file(s) are available! There are
no reliable atomic coordinate data for many excellent topics!
- 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.
- 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.
- 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
example, my DNA
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.
- 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
provides links to explanations of all commands.
- Poor design:
For reference documents on commands for Protein Explorer (PE),
- All sources must be cited.
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 (pubmed.gov). Search at
and when you find the paper, copy the URL and paste it into a link, for example
PDB filenames can be linked to the Protein Data Bank by substituting
their 4 character
code at the end of
You may prefer also to cite the original papers for PDB files featured
in your web presentation, e.g.
Marmorstein et al., 1992), although the original paper is linked to the
Books should be cited fully and hyperlinked to the publishers page
for the book if you can find it.
- 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
in his class
Macromolecular Visualization in fall [year]."
- 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.
We're not talking about just linking to other people's sites,
which they're always happy to have you do. We're talking about
actually copying for example
a GIF or JPG file into your presentation. For example,
in 1999, a student in my class, Stefan Welte, scanned an image from a book
(see in his
web presentation the
- 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
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: . There are examples for
Antibody: click on Immunoglobulin Domain).
with color-matched text.
- Good design:
- Bad design:
blue, T is
yellow, G is
green, and C is
- Horrible design:
blue, T is
yellow, G is
green, and C is
- Use colors that stand out against the background: avoid
blue on black! The most common error is to use pure blue
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.
- 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
If you use
a nonstandard color scheme, there should be a compelling reason.
- All PDB files greater than a few kilobytes in size should be
Gzipping PDB files for Chime
at the UMass Chime site FAQ.
Recommended (but not required)
- 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.
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.
has been developed by
Craig Martin for his
Biomolecular Structure course. Don't attempt to
unless you can afford to spend a lot of time on it!
- 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
zoom to carbohydrate within antibody (click on "Whole IgG1,
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
Chime command reference manual.
Checklist of the above topics:
- Molecule not in Chime on the web already?
- Talk not more than ten minutes?
- Main point of each image clearly stated?
- Links describe resource (not "click here")?
- Sources cited and hyperlinked?
- Contributors acknowledged?
- Permission obtained to include any items authored by others? (Does not
apply to hyperlinks.)
- All (or most) buttons independent?
- All color schemes keyed with color-matched text?
- No blue on black!!
- Color schemes standard? (DRuMS!)
- All PDB files gzipped?
- Short and simple?
- Use template provided.
- Long movie sequences avoided or justified?