A mythological molecular modeller
July 2, 2006
Chimera is a free and multiplatform molecular visualization program with extensible capabilities and several interesting features.
With Chimera you can use several render modes such as: stick, ball-and-stick, CPK, ribbon, a special nucleotide representations and molecular surfaces. Other interesting graphics features are the ability to translation, scaling, and rotation and stereo viewing. You can use standard color modes ( RGB, CMYK, transparency, etc ) to colour yout model.
With Chimera you can easily add hydrogen atoms and its comes with a powerful high-quality hydrogen bond identification algorithm. Interactive bond rotation, distance and angle measurements is also possible.
Chimera can display 3D data acquired via electron and light microscope, x-ray density maps, electrostatic potential and other more. You can also sclice and segment your model. Morover, with the Multiscale extension, you can display molecular complexes and quaternary structure.
It is also possible to display molecular dynamics trajectories simulation with the Amber8 Sander module.
Docking analisys is possible via the ViewDock module that allows to view molecules in binding site and that permit to screen ligand candidates by hydrogen bonds.
Chimera also comes with the powerful Multalign Viewer extension that permit multiple sequence alignments and calculates consensus sequence and conservation histogram. You can also superimpose a structure based on the sequence alignment.
Using Collaboratory extension, Chimera can also work in a distributed computing environment that allows to conduct a shared molecular modelling session over a standard network connection.
Finally, Chimera has powerful and extensible programmable core. You can interact with all Chimera functions through Python script and so you can implement your own algorithms and extensions.
Screenshots and Animation gallery is aveible here and here.
Here you can find a Command Quick Reference Sheet ( pdf ).
Two Chimera tutorial is aveible here and here.
A guide to Volume Data Display here.
Here you can find the Chimera Programmer’s Guide with python extension examples.
The latest Chimera version is 1.2199 and it is aveible here for Linux, SGI IRIX, HP Tru64 Unix, Mac OS X and Windows.
