Tables for
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 25.2, p. 725

Section The coordinate system

P. J. Kraulisr* The coordinate system

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The viewpoint in the MolScript right-handed coordinate system is always located on the positive z axis, looking towards the origin, with the positive x axis to the right. The user obtains the desired view of the structure by specifying rotations and translations of the atomic coordinates; it is not possible to change the location or the direction of the viewpoint.

There are two main benefits with this scheme: The first is that it is similar to the way we handle objects in everyday life: we do not normally fly around the object, but rather move it about with our hands. The other benefit is that together with the coordinate copy feature it can be used to compose an image containing several geometrically related subunits.

The disadvantage is that the atomic coordinates must be transformed before the creation of the graphics objects. This may complicate the composition of an image where another structure or geometric object is to be included. For example, if two separate structures have been aligned structurally by some external procedure, then the user must take care not to destroy the alignment in the process of setting the viewing transformation.

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