Summary of some of the currently available visualisation software
(John Tate, Molecular visualisation , Structural bioinformatics (2003; edited by Philip E Bourne and Helge Weissig)
Name
AVS
Capabilities Comments
Structure
query,
presentation
Complex and extremely
powerful framework for
building custom applications
using modular program
fragments.
Pros
Cons
Platform
Extremely flexible.
Expensive and
cumbersome.
Linux
SGI
Unix
Provides many powerful
modules for all kinds of data
manipulation and analysis
Difficult to learn
Commercially available and
supported
Bobscript
Presentation
An enhanced version of the
original MolScript
Powerful command language.
Attractive representation styles.
Improved colouring capabilities
relative to MolScript v1.
Command syntax can be
unintuitive.
Linux
SGI
Unix
Lacks the OpenGL
preview mode of
MolScript v2.
Supports electron density maps
Chime
Browser-plug
in version of
RasMol
Commercially developed
version of RasMol, designed
to operate as a plug in for
Netscape.
Operates under some version
of Internet Explorer, via the
Netscape-style plug-in
architecture.
Same power and flexibility as
Rasmol
Web based
Available for only a
limited number of (nonUnix) platforms.
Commercial, closed
source package.
Apparently no longer
under active
development.
NT4.0
W2000
Mac
Chimera
Dino
Grasp
Basic model
building,
model query,
presentation
Presentation
A modular package for all
aspects of molecular
visualisation, from simple
model building through
production of high-quality
images
Flexible and extensible.
Closed source.
Powerful tools, such as the
docking module, are already
available.
Still in fairly early stages
of development.
NT4.0
W2000
Linux
SGI
Unix
Powerful and flexible generalpurpose visualisation
program.
Flexible representation styles.
Visually very attractive
representations.
Still underdevelopment so
bugs are quite common,
although rapidly fixed.
Linux
SGI
Unix
Capable of displaying
everything from protein
structures to macromolecular
surfaces to topology data
from TEM
Output in a range of formats,
including various image
formats, postcript and povray.
Quirky command
language can be difficult
to learn
Support for a wide range of data
sets, including general volume
data, such as cryo-EM data.
Electrostatics
Widely used program for
Can generate and display
calculation and
looking at molecular surfaces
molecular surfaces easily.
representation
and electrostatics. Somewhat Reads potential data calculated
dated now.
in standard electrostatic
programs.
Complex command
language.
SGI
Unintuitive user interface.
No longer under active
development.
Closed source and only
available for SGI.
MICE
Java applet for
structure
display
Lightweight structure viewer
with collaborative
capabilities.
Simple to generate attractive
Requires Java3D, an nonand detailed views of
standard Java extension
structures via a form interface.
that is available only on
certain platforms.
Can access any structure in the
PDB from just an ID code.
Web deliverable.
Collaborative.
Limited tools for querying
structures.
NT4.0
W2000
Linux
SGI
MolMol
MolScript
Presentation
Structure
interrogation
Presentation
Graphics program for
displaying, analysing, and
manipulating the threedimensional structure of
biological macromolecules,
with special emphasis on the
study of protein or DNA
structures determined by
NMR
Reads various file formats.
Preparation of figures, as
simple schematics or, in
conjunction with Raster3D,
ray-traced images.
Powerful command language.
Both command line and mouse
driven.
Command syntax can be
unintuitive
NT4.0
W2000
Linux
Unix
Command syntax can be
unintuitive.
Linux
SGI
Unix
Possible to write visually edited
PDB files.
Very high quality output
(PovRay).
Attractive representation style.
Wide range of output formats.
Apparently no longer
under development.
An OpenGL front end allows
interactive previewing of
scenes.
O
PyMol
Electron
density map
interpretation.
Model
Building
Extremely powerful, if
somewhat unintuitive,
model-building package.
Presentation
Some presentation capabilities.
Flexible, configurable interface.
Can be difficult to learn
and use well.
Large user base and good
discussion groups available.
Closed source
Powerful python-based
visualisation program.
Wide range of attractive
representation styles.
Can be difficult to learn.
Input is via both a graphical
user interface and a pythonbased command language.
Flexible command languages.
One of the most widely used
model-building packages,
certainly in academia.
Extensible.
Open source.
Runs anywhere that runs
python.
Fairly heavy on memory
and CPU resources, so a
powerful computer is
needed to do the
program justice
NT4.0
W2000 (?)
SGI
NT4.0
W2000
Mac
Linux
SGI
Unix
Quanta
Model
building.
Structure
interrogation
Commercial package for
constructing, modifying and
interrogating atomic models.
Wide range of tools for all
aspects of structure work.
Widely used in industry but
less common in academia
because of the cost.
QuickPDB
Structure
query
Simple structure and sequence
display tool.
Small and quick-to-load Java
applet
Structure
interrogation.
Presentation.
Basic
modelling
SGI
Older software, lacking
many of the newer
features of other
comparable packages.
One of few tools that allows
consideration of structure and
sequence simultaneously.
Web deliverable.
Users an older version of Java
that is embedded in many
older versions of the popular
Web browsers, making it
largely platform independent.
Swiss PDB
viewer
Commercial software,
subject to license fees.
Expensive, even for
academic users.
Swiss-PdbViewer is an
application that provides a
user friendly interface
allowing to analyse several
proteins at the same time.
The proteins can be
superimposed in order to
deduce structural alignments
and compare their active sites
or any other relevant parts.
Loop database available.
POV-Ray scenes can be
generated from the current
view.
Reads electron density maps,
and provides various tools to
build into the density.
Possible to thread a protein
primary sequence onto a 3D
template and get an
immediate feedback.
Very basic.
NT4.0
W2000
Mac
Linux
SGI
Unix
Molecular graphics not the NT4.0
W2000
most impressive.
Mac
Linux
SGI
Unix
Rasmol
Structure
interrogation.
Presentation
Lightweight but very powerful
interactive structure viewer.
Quick, responsive interface.
Powerful command language.
The Swiss-Army knife of
Wide range of representation
macromolecular visualisation
styles.
Open source and freely
available – still developed (to
a certain extent) and
maintained by users.
RasTop
VMD
Enhanced
RasMol
Structure
analysis and
presentation,
with an
emphasis on
molecular
dynamics
Improved version of RasMol,
with many additional
features such as an improved
user interface, mouse-based
selection, better support for
animation.
Improved appearance over
original RasMol.
Includes numerous tools for
dealing with molecular
dynamics, trajectories and
models.
Can be completely mouse
driven, but also includes a
powerful scripting language
that can be used to extend the
program and automate
procedures.
General-purpose interactive
visualisation
Shows only one structure
at a time.
Ugly graphics – not really
suitable for presentation
or publication any more.
NT4.0
W2000
Mac
Linux
SGI
Unix
Unlikely to be adapted to
make it Web deliverable
(although see chime) or
to give it significantly
more features.
Windows only
NT4.0
W2000
Rather slow without a
powerful machine with
good graphics
capabilities.
NT4.0
W2000
Mac
Linux
SGI
Unix
Corrects a number of serious
deficiencies with original.
User interface removes the need
to learn the command
language.
Easy to use for simple
visualisations.
Supported and documented and
still under active
development.
Largely aimed at
molecular dynamics.
WebMol
Xfit
Java applet for
structure
display
Electron
density map
interpretation
Model
building
Presentation
Lightweight and quick Java
applet. Simple display styles
only, but some sophisticated
tools for structure
interrogation
Web deliverable – no
installation required.
Part of XtalView
crystallography package.
Completely mouse driven.
Sports a comprehensive set of
model building tools, most
notably the ability to
generate electron density
from structure factors on the
fly.
Can load structures from URL
or local files.
Limited display styles.
Apparently no longer
under active
development.
Platform independent – runs
wherever Java is available.
Integrated into XtalView and
therefore able to rapidly
exchange data with other
XtalView packages.
Fairly lightweight compared to
other model-building
packages.
Can be difficult to find
commands and features
in the maze of panels
and buttons until
familiar with the
program.
Largely undocumented.
NT4.0
W2000
Mac
Linux
SGI
Unix
Linux
SGI
Unix