Chimera Keyboard Shortcuts (Accelerators)

Keyboard shortcuts are disabled by default, but can be enabled:

• with the command ac
• by starting Keyboard Shortcuts (for example, with Tools... General Controls... Keyboard Shortcuts) and turning on Enable keyboard shortcuts; this also enables shortcuts automatically in subsequent uses of Chimera

Notes

ab and ai - superimpose and compare backbone segments that have the same sequences, numbering, and chain identifiers.

Atoms from exactly two models must be selected, and atoms other than CA (proteins) and P (nucleic acids) are ignored. Only atoms with the same name, residue type, residue number, and chain identifier are paired; ab performs a least-squares fit and applies the resulting transformation, whereas ai does not apply the transformation but shows it with two rectangular slabs colored to match the structures. Both ab and ai report the RMSD, number of atom pairs, and angle of rotation in the status line and Reply Log.

One application is to measure changes in relative domain orientation in different conformations of a multidomain protein. For example, the thioredoxin reductase structures 1f6m and 1tde differ by a rotation of one domain relative to the other. They are different conformations of essentially the same protein and are numbered in the same way (chains other than A can be deleted). After selection of one domain (approximately residues 1-117, 245-320) in both structures, ab could be used to superimpose that domain. The selection could then be inverted to encompass the other domain (approximately residues 118-244) in both structures and ai used to compute the transformation, in this case a rotation of ~67°. This conformational change is described in Lennon et al., Science 289:1190 (2000). The two accelerators do not have to be used together; the first domain could be superimposed manually or with MatchMaker before ai is used to compare the orientations of the second domain.

bv - Extend periodic map to cover selected atoms.

Creates a new map that covers the currently selected atoms plus 5 Å padding on all sides. The map is derived from the current set of data (active map) in Volume Viewer. If the atoms plus padding extend beyond the bounds of the active map, then it is assumed that the active map is periodic along all three axes (such as a unit cell crystallographic density map). The new map is displayed using the thresholds and colors of the original map and the original map is undisplayed.

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 calculation has been implemented in C++ for better performance.

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.