What are Rasmol, CHIME, and Jmol?

The program Rasmol runs on both Macintosh and Windows platforms and allows one to display protein and nucleic acid structures. It has a long history and can be downloaded in various versions. It allows one to manipulate structures in the sense that one can change coloring, representation, turn elements on and off, and interogate structures. One cannot in any way change a structure using Rasmol.

Rasmol, in turn, inspired a browser-based plug in, CHIME, with the same functionalities, using almost the identical command set. Thus going back and forth between the two easy.

CHIME allowed the creation of a WEB-based (and CHIME-based) exploration tool called Protein Explorer. This package is widely used and very powerful. A limitation of CHIME (and of Protein Explorer) is that you must install a plug-in into your browser. A more serious limitation is that development of CHIME has stopped and will likely not continue. As a consequence, there are limitations regarding which browsers work on specific platforms.

Most recently, a new browser-based alternative has arisen, inspired by Rasmol and by CHIME This software, Jmol, also runs on both platforms (and Unix, et al.). It exists both as a stand-alone JAVA application and as a browser-based function. Note that for the browser function, you don't need to download anything to your computer - the software is automatically downloaded when you access a Jmol-enabled site (don't worry, it's safe). Again, the command set is based on Rasmol/CHIME, so the transition should be easy.

A different program, available on both platforms, is Swiss PDBViewer, or DeepView. This program is excellent at viewing structures, but also allows for some manipulations. For example, this program will allow homology modeling. There is no browser-based version, so this is not good for preparing presentations of structure.

See the site MolviZ.Org for more detailed descriptions of these and other software.

Finally, various presentations have been prepared for this course using CHIME and some of these will be converted to Jmol format. These are listed below. Also listed is download information for pre-prepared packages for creating presentations in either CHIME or Jmol

CHIME-based:

Presentation package: CHIMEShell
Protein Explorer
Immunoglobulin binding protein - a very simply alpha/beta protein
Arc repressor - up-down beta protein
Alpha beta crystallin - a Greek Key example
Arabinose binding protein - an alpha/beta protein
Homeodomain protein - a H-T-H DNA binding protein
Retinoic Acid Receptor - multimeric H-T-H DNA binding protein
IHF - a DNA binding/bending protein
Plastocyanin - a Cu2+ binding all beta protein
Pectate lyase - Big, mostly beta protein
Thermostable phytase - a student presentation on a complex protein
Cytochrome c oxidase - a complex membrane, metalloprotein
Maltoporin - an all-beta transmembrane channel

Jmol-based:

Presentation package: JmolShell
Winged Helix - DNA binding protein
lac repressor - A multimeric DNA binding protein
CRABP (cellular retinoic acid binding protein) - beta clamshell