RasMol is famous for
Chime retains most of these great features*. Because it is a Netscape plug-in, molecular structure tutorials using Chime can be viewed as ordinary web pages. This makes them more easily accessible than are RasMol "movie" scripts. By virtue of being embedded in web pages, Chime removes many limitations which RasMol places on educational tutorials. In addition, enhancements to RasMol's scripting language which have been implemented in Chime make it far superior to RasMol for educational scripts. And Chime has other new capabilities not found in RasMol.
*Exceptions: Chime's source code is proprietary; RasMol is
faster than Chime under Windows 3.1x only.
Who made Chime, and why is it free?
Chime is the product of MDL
Information Systems, Inc., a software company specializing in
databases and information management systems for the pharmaceutical
and chemical industries. One of their products, Chemscape, provides
structure and text searching via a web browser into a client's
database. Chime Pro, a commercial product, was built as a
molecular structure viewer to inteface with Chemscape. Chime
1.0, lacking the Chemscape interface was made available free to all
users. This benefits MDLI by increasing the visibility of their
company and their products, while simultaneously benefitting the
scientific and educational communities at large.
Chime is Built upon RasMol
Tim Maffett, Chime's principal architect at MDLI, used 16,000 lines
of RasMol's C source code as part of the infrastructure of Chime.
This was possible because Roger Sayle, RasMol's author, had
generously placed RasMol's source code into the public domain. For
use in Chime, the RasMol source code was converted to C++ and
modified to become reentrant (which allows multiple Chime plug-in's
to run simultaneously, even on a single web page). Maffett and
other programmers at MDLI added over 100,000 lines of original C++
code to create Chime.
What Chime Has that RasMol Lacks
Probably the most important enhancement Chime adds to RasMol functionality
is being a plug-in. As explained below, this has enormous benefits for
educational tutorials. However Chime also added wholly new features
including:
Advantages of Chime over RasMol for Educational Tutorials
Flow control: hypertext, buttons, nonlinearity. RasMol
scripts have very limited flow control. They can only move
forwards (not backwards) through a linear path (no branches, no
hypertext).
By virtue of being a plug-in, the HTML environment in which Chime is embedded allows flexible flow control. Backing up can be as simple as reloading a web page. A hypertext-linked table of contents, or a group of text-labeled buttons can allow entry into a script at any user-selected point. Thus, the progression of a user through a tutorial can be nonlinear and tailored to the user's needs and interests.
Legends: color-keyed, font control. RasMol's echo command can write multiple-line text legends to accompany the molecular graphic. However, these legends cannot be in color. One of the powerful features of RasMol is the use of consistent, highly informative color schemes. For example, the CPK (Corey Pauling Kultin) scheme allows identification of the element for each atom. One needs a legend which identifies oxygen as red, nitrogen as blue, carbon as gray, etc. Such a legend is enormously more effective when in color, which cannot be done in RasMol.
|
|
RasMol's legend font is fixed. On high-resolution displays, it becomes too small to read when projected.
The HTML control of legends on a Chime web page allows full color and font size control. Here is an example, a linear tutorial on Protein Secondary Structure.
Unlimited, independently scrolling, descriptive hypertext. Text descriptions within RasMol are limited to a few lines echoed to the command line window (see legends, above). MAGE allows more extensive text, but not true hypertext. With Chime, unlimited, independently scrolling hypertext can be in a separate frame adjacent to the graphic. Buttons embedded in the text control the graphic by sending script segments to Chime. Here is an example by David Marcey on DNA Polymerase.
Hardware-independent timing. The speeds of movements in RasMol scripts are hardware-dependent. When a RasMol script is run on a computer different than the one on which it was developed, often it runs far too fast or too slow. Adjusting the timing in a RasMol script typically takes several hours. Chime provides clocked moves and delays which occur in specified time intervals, independent (as much as possible) of hardware speed. (Slow machines have less smooth movements, which may exceed the desired time; fast machines have smoother movements which never occur in less than the desired time.)
User movement without misorienting subsequent script. In
RasMol scripts, when standing at a pause, the user can rotate, zoom,
and slab the molecule with the mouse. However, when continuing, the
molecule may be left misoriented. Preventing this requires tedious
hand-coding to restore the pre-pause orientation after the pause.
Therefore, few RasMol scripts do this consistently. Chime's new
view save and view restore commands make this easy.
Advantages of RasMol over Chime
Interactive interface. RasMol's superb user interface is the
best way to explore interactively a PDB file ("molecule") of your
choice. A command-line interface
can be provided for Chime, but the PDB files available must be
pre-programmed, so you cannot load any arbitrary PDB file of your
choice. In any case, unprogrammed interactive exploration is more cumbersome
in Chime than in RasMol.
Automatic saving of scripts. RasMol's save script filename command automatically saves a script which, when played back, regenerates the exact view present at the time the script was saved. This is a very powerful feature which is necessarily lacking in Chime for web security reasons. RasMol-saved scripts will play back in Chime! Thus, saving scripts with RasMol and then playing them back in Chime is the easiest way to make a Chime presentation.
Speed. RasMol 2.6b2 can be twice as fast as Chime 1.0 under Windows 3.1 with a rotating spacefilled image, provided 32-bit RasWin is used (requiring the free Microsoft accessory Win32SOle; 32-bit Chime runs only under Windows 95). This makes RasMol more useful on slower computers. Under Windows 95, Chime is about 20% faster than RasWin32 at rotating a spacefilled image.
High-Resolution Printing. As of Chime 1.0, plug-in images can be printed at screen-resolution on all platforms except Windows 3.1. However, Chime offers none of RasMol's Export options such as vector postscript, needed for high-resolution printing.
Saving GIF images. RasMol's Export menu allows saving the current graphics image into a compressed Compuserve Graphics Interchange Format (GIF) file. Such files are needed, for example, to place an image on a web page. Chime has no Export menu.
No web browser needed. RasMol runs by itself. Unlike chime, you don't need to run Netscape to use it.
Source code. RasMol's source code is in the public domain. This has allowed individuals to modify RasMol (e.g. Molinaro's Berkeley RasMol which loads multiple molecules and moves them independently) or to port RasMol to other platforms (e.g. Acorn RISC OS), or to use RasMol features in other programs (e.g. Chime and MSI's WebLab). Chime source code is proprietary to MDL.