Z Flip for Models and Maps

Z-Flip for models and maps

It is a well known phenomenon that calculated reconstructions in electron microscopy have ambiguous chirality, due to the symmetry of projection images (parallel and antiparallel projections are indistinguishable).

Maps (partial or otherwise) used in processing of particle images should have the same handedness as the final reconstructions output by programs such as Relion. However, deposited maps and atomic models will always have the correct, physical handedness, in which amino acids are L and alpha helices are right-handed.

Maps can have their handedness exchanged using the so-called "Z-flip," in which the grid is mirrored across the XY plane. In UCSF Chimera, maps are easily flipped using the command vop zFlip model-spec, where model-spec specifies one or maps (e.g. vop zFlip #0).

Certain tasks, such as map preparation for projection subtraction, may require fitting an atomic model directly into raw output maps. Unfortunately, there is no simple command to Z-flip an atomic model, in the case where the raw map is "backwards." Instead, the following method has been developed:

1. Run UCSF Chimera, open raw map and atomic model coordinates.

• Tools > Genera > IDLE.
• Replace the 0 in openModels.list()[0] with the appropriate model specifier, then copy and paste:

m = chimera.openModels.list()[0]
for a in m.atoms:
    crd = a.coord()
    crd.z = 0 - crd.z
    a.setCoord(crd)

The atomic model will be flipped, and may then be fit into the flipped density map. Chimera is unable to properly display backwards helices, so the model will appear strange, but the coordinates will be correct.