On Apr 26, 2005, at 8:47 AM, Jesse Parker wrote:

I am currently looking for ways of visualizing proteins as they are being folded by a matlab program we are developing here at the University of Connecticut. I am unsure whether an extension would be adequate to read and write to matlab, or modifications to the chimera source would be necesarry. Would it be possible to get a copy of the source code for Chimera and possibly some examples of extensions?

Hi Jesse, An extension should be adequate to do what you want. Chimera was designed from the beginning to be as extensible as possible and the bulk of Chimera's functionality is provided as extensions. The best place to get started in finding out what extensions can do is to look at the programming examples, which you can find as link off of this page: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html . The FAQ off of that page can also be useful. We also try to answer any questions going to this list. All the Python source code is actually provided with your Chimera download. Beneath your Chimera installation directory (which can be tricky to reach on a Mac -- use Terminal) there is a directory named "share" which contains all the Python source code. Many complex extensions are written entirely in Python (e.g. FindHBond, MultAlign Viewer). Some extensions do make use of compiled code, typically for speed, but even there the Chimera C++ isn't modified; instead a Python compiled shared library is created (one of the programmer's examples deals with this) and is loaded on demand by the Python part of the extension. We don't distribute the C++ part of Chimera basically because it would be a miracle if anyone else could get things set up so they could compile it. We do provide the header files for download so that people can more easily determine the methods that various classes offer (the link is also off the page above). We are in the process of making the source files available to some developers, so that they can determine exactly how certain functions operate. If you needed that kind of access also, we could probably add you to the access list when it's ready. In the (hopefully unlikely) case that you actually need a modification to the Chimera C++ source, it would probably be easiest for you to request the change from us, and for us to make the change and compile a new version and send it to you. If you do wind up writing your extension for Chimera, we would really appreciate it if you could drop us a line saying that you did. Things like that look really good on our grant-renewal application! :-) Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu