Chimera Configuration and Tricks

The first thing you will inevitably need to do in any molecular rendering software is to configure your background to white (who ever wants an unpublishable black background?, ever?), the atom colors to the standard CPK colors for atoms (the curse of the green carbons follows chemistry everywhere!) and no perspective so that a cylinder, for example, will become a circle when viewed from the top. So, in chimera the file where your preferences reside at is:

.chimera/preferences

But there seems to be no way to store easy commands such as:

set bg_color white

In there. And one needs to save setups via preferences which result in the following hard to read syntax:

'Background': {'Background color': (1.0, 1.0, 1.0, 1.0),
                'Background gradient': (('Chimera default',
                                         [(1, 1, 1, 1), (0, 0, 1, 1)],
                                         1),
                                        1),
                'Background image': (None, 1.0, 2, 1)},

It seems like the only way around this is to create a startup script for chimera which will include the --preferences command pointing to a file with the easier command line settings.

- Links

- Setting preferences.