Chimera
Tuesday Morning Practical
Chimera is a comprehensive tool for molecular/macromolecular visualization. It will be used as a complementary tool throughout the workshop, and will be required to fully participate in the practical sessions.
Tom Goddard, developer of Chimera volume capabilities will give the tutorial.
Installing Chimera
For the Tuesday, March 15 Chimera tutorial we will use Chimera production release 1.5.2 (or 1.5.3 is also ok if it is released before the workshop). Download and install it from the
There are 32-bit and 64-bit versions of Chimera on Linux, Mac and Windows. The 64-bit versions require Windows 7, or Mac OS 10.6 or 64-bit Linux. The 32-bit and 64-bit versions will work equally well for this tutorial. For large data sets (maps > 512 Mbytes) the 64-bit versions are preferred.
On Linux the installer is an executable (with ".bin" file suffix) that you run from a command-line. You may need to make it executable after you download it using unix command "chmod a+x chimera*.bin" in order to be able to run it.
On Windows the installer presents a standard graphical user interface that you click through.
On Mac the Chimera is distribution is a dmg file that you open then drag the Chimera application to wherever you want to put it.
After installing, you can check if Chimera is working by opening a molecular model or a density map, for example, start Chimera and use menu entries
- File / Fetch by ID / PDB / 6bna
- File / Fetch by ID / EMDB / 1094
Chimera Tutorial Data
We'll look at fitting, symmetry, and visualization of Rous sarcoma virus capsid protein. Here are some data files we will use (EMDB 1862, PDB 1em9, 1eoq, 3p05) and an HTML outline of the tutorial in a zip archive.
Rous sarcoma virus is a retrovirus that causes cancer in chickens. It's capsid protein is similar to that of HIV and forms irregular polyhedral capsids.
We'll follow the analysis in the following publication.
Visualization of a missing link in retrovirus capsid assembly.
Cardone G, Purdy JG, Cheng N, Craven RC, Steven AC.
Nature. 2009 Feb 5;457(7230):694-8.
Here's a screen-capture video covering the steps in this tutorial (48 minutes, 270 Mbytes, H.264/MPEG4, download mp4).
During the tutorial I will present the steps live so the video will not be needed. But it will be useful for future reference, or if the participants miss some steps during the tutorial.