Protein Explorer and Chime Resources
Guide for the Center for Molecular Modeling, NIH, January 2001
from Eric Martz, University of Massachusetts, Amherst MA USA
Most of the software below is open-source freeware, and can be used
directly from the web, or downloaded for off-line use.
Most was supported by the National Science Foundation.
This guide is available on-line:
(PE) version 2.0 enables visualization of macromolecular 3D
structure with exceptional ease of use. Visual analysis of proteins,
nucleic acids, and ligand interactions can be done largely from menus,
buttons, and forms, with context-sensitive help and color keys displayed
automatically. PE employs the Chime plugin that is derived from RasMol, and
PE understands all RasMol commands. However PE enables visual analysis to
considerable depth without learning a single RasMol-style command, and it
is much more powerful than RasMol. PE enables easy selection of portions of
a molecule, to apply different rendering or coloring schemes, and to hide
selected moieties. In addition it has one-click routines to map sequence to
structure, show contact surfaces (overview of noncovalent bonds to any
moiety), solvent-accessible surfaces, cation-pi interactions, and salt
bridges. Advanced routines simplify finding noncovalent bonds, and coloring
a protein by conservation/mutation from a multiple protein sequence
Websites can include hyperlinks to Protein Explorer that
prespecify molecule(s). Adopted by the Protein Data Bank as a 3D
structure viewer. Authored by Eric Martz, using MDL Information Systems'
Chemscape Chime freeware. PE is freeware for Windows or Macintosh.
A search interface for the Protein Data Bank designed for students,
educators, and occasional users. Jargon is avoided or explained.
Detailed instructions for downloading PDB files so you can open them
in RasMol or Protein Explorer. Tabular summary is easy to scan. Disallows
syntax that gives false misses. Automatic synonym searching ("hemoglobin"
finds "haemoglobin"). Mirrored around the globe. Authored by Eric
Martz and Jaime Prilusky in 1998; upgraded by Jaime Prilusky in 1999-2000 to work
with the OCA browser.
World Index of Molecular Visualization Resources.
"Visitor-Maintained": additions or changes supplied
by visitors via web form are immediately alphabetized into the
subject and author indices. Visitors can enter hyperlinks,
describe the resource, and provide subject or molecule name
Categories include Biochemistry, Organic Chemistry, Inorganic Chemistry
and Crystals, How To
Create New Chime Resources, Sources of Molecules (PDB files), K12 Resources,
Swiss-PDB Viewer Resources, Molecular Galleries, EMail Lists, Non-English
Resources, Free and Commercial Software.
Visitor-Maintained Indices program authored by Trevor
Kramer and Eric Martz.
Displays morphs of protein conformational changes as "movies". Examples
include the binding of calcium to EF hands, and the resulting conformational
change in recoverin (a calcium-activated myristoyl switch). Instructions
are provided for creating your own morphs using linear interpolation or
"chemically plausible" intermediates calculated with software by
Werner Krebs and Mark Gerstein (Yale) or Gerard Kleywegt (Uppsala).
The resulting morphs (in NMR PDB format) can be most easily played as movies
in Protein Explorer.
NonCovalent Bond Finder.
An automated tool in Chime that finds the closest contacts
between any two sets of atoms. Pressing the [Find] button
repeatedly steps out in 0.1 Angstrom increments. Fill out the
residues to which atoms belong in a single click. By Eric Martz,
released in 1998.
www.umass.edu/microbio/chime/find-ncb (also available within Protein Explorer)
Biochemistry in 3D.
A new, superb, state of the art Chime website with interactive tutorials
on protein architecture (from amino acids through peptides, secondary, tertiary
and quaternary structure), trimeric G proteins, bacteriorhodopsin, myoglobin
and hemoglobin, and restriction endonucleases.
Written by Tim Driscoll, Freida Reichsmann and others.
Additional tutorials on protein structure, DNA and DNA-binding
proteins authored by Frieda Reichsman are at the second site below.
DRuMS Standard Color Schemes for Macromolecules.
A proposed standard set of color schemes for proteins and
polynucleotides authored by Tim Driscoll, Frieda Reichsman, Eric
Martz, and Roger Sayle. Freely available for educational or
commercial use. Adopted in Protein Explorer, and Biochemistry in
3D (see below). Website provides rationales, demonstrates color schemes
on variety of molecules, and offers for download Chime scripts
that apply the color schemes to any molecule.
Presentations in Protein Explorer (under development).
Support for tutorials and molecular structure presentations within
Protein Explorer is under construction.
Collaborations are planned for visualization of
protein structure research and
bioinformatics results. Parties interested in such collaborations
are invited to contact
The tutorials will appear
similar to most existing Chime tutorials (see the World Index above)
with buttons producing a series of author-prepared images in Chime.
However, from any image in the tutorial, one can move seamlessly into
Protein Explorer, then back into the tutorial.
Prototype demonstrations: SV-40 Capsid assembly
from 360 copies of the VP1 protein monomer, by Stefan Welte.
Bacterial Cell-Division protein FtsZ by Gabe McCool.
High-Detail Physical Molecular Models.
3D Molecular Designs manufactures high-detail molecular models from atomic
coordinate files. A computer model is converted to an engineering format (stereolithography),
which instructs a selective laser sintering machine to create a nylon model
(see figure at
Protein Explorer for Novices:
Advanced Protein Explorer: