Chimera Keyboard Shortcuts (Accelerators)

Keyboard shortcuts are disabled by default, but can be enabled by choosing Tools... General Controls... Accelerators On from the Chimera menu. To enable shortcuts automatically in subsequent uses of Chimera, open the Tools preferences, check the Auto Start option for Accelerators On, and Save the preferences.

Notes

Im - Invert map values.

If the map value type is signed (e.g. 32-bit float or signed 16-bit integer), each value is multiplied by -1. For unsigned 8-bit maps, the values are multiplied by -1 and 255 is added so that the values remain unsigned. For other unsigned maps, the values are multiplied by -1 and the maximum map value is added so that the map remains unsigned. The accelerator acts on the current set of data in Volume Viewer. A copy of the map is made unless the map is itself a copy (for example, made using wv, zb, or Volume Eraser). The original file is not modified. Use the volume dialog menu (File... Save map as...) to save the inverted map.

sd - Measure distance from selected atoms/markers to surface.

The distance from each selected atom or path tracer marker to each displayed surface is printed in the Reply Log. Example:

Distance from #0:18.water@O to surface MSMS main surface of 1a0m.pdb
 d = 2.09, surface point (3.14, -1.28, 7.85), side 1

The coordinates of the nearest surface point and the side of the surface that the point lies on (+1 = outside, -1 = inside) are given. The closest surface point may lie within a triangle, on a triangle edge, or at a triangle vertex of the triangulated surface. If multiple surface points are equidistant, only one is reported. The closest-point calculation is in Python and is rather time-consuming (~1 second for one distance to a 10,000-triangle surface on a 2006 desktop PC). The distance calculation code may be rewritten in C++ in the future.

u8 - Interpret MRC signed 8-bit map as unsigned.

The MRC volume file format does not support unsigned 8-bit map values. Some EM tomography programs use it to hold unsigned 8-bit values (0-255) with the data type in the file header incorrectly indicating that the values are signed 8-bit (-128 to 127). Use the u8 accelerator to reinterpret the data values as unsigned 8-bit. The original file is not modified. The accelerator acts on the current set of data in Volume Viewer. It only works on MRC format maps.