PREABS : Interactive crystal shape manipulation

Authors: Doug du Boulay

Contact: Doug du Boulay, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia

PREABS is a screen-based interactive X11 display routine for checking and viewing the crystal shape description required for ABSORB. The diffractometer axes may also be rotated.

Overview

PREABS is a work in progress. It is intended to permit graphical editing of crystal size and shape in order to accurately model real crystals of ill defined shape. Unfortunately the editing aspect of this program has not been completed. It does however, permit visualization of crystal models constructed via the usual ABSORB face description methods. The crystal model is displayed, embedded within the ABSORB, internal, equivalent diffractometer specification, corresponding to the Busing and Levy (1967) system. The overall view of the crystal and diffractometer can be rotated with left-mouse-click-drag events, and by switching the right-mouse-button mode, the crystal can be rotated about specific diffractometer circle axes. The position of the telescope is adjustable and an image of the crystal through the telescope can be obtained.

Figure 4.4. Screen shot of PREABS

Screen shot of PREABS

General control functionality

ZERO AXES

This control reset all diffractometer angles to zero

CELL AXES

Switches on/or off both the reciprocal and real space axes on the model

DIFF AXES

Switches the diffractometer coordinate systems on or off. This is a four mode switch, since both the XTAL coordinate system and the actual diffractometer coordinate system may be different. Setting 0 switches both axes systems off. Setting 1 switches the XTAL coords on, setting 2 switchesthe real coords on, while the final setting displays both sets of axes. Drawing the real diffractometer axes requires the presence of the original UB matrix used to measure the reflection data on the xtal archive.

ANIM On/Off

Activating the ANIM option switches on animation. In this mode, and left-mouse-click-drag-release events are converted to angular momentum, and the diffractometer as a whole is set spinning. To stop a spinning image, simply left-click-release with no mouse motion. Reselecting ANIM , switches this mode off.

ZOOM MODE

Currently has no functionality

FILLED

Switches filling of the front display surfaces of the diffractometer circles on or off. This can result in significantly slower rendering.

BACK HIDE

This control switches on or off the display of diffractometer faces which face away from the viewing direction.

PERSPECTIVE

Currently has no functionality

FACE NORM

This control switches on or off the crystal face normals and their associated approximate miller indices.

TELESCOPE

Activating the TELESCOPE mode, temporarily changes the functionality of the right mouse button, such that by right-mouse-click-drag-release events, the position of the telescope can be dragged to an orientation corresponding to that on the actual measurement diffractometer. The telescope can then be locked to move synchronously with the omega axis, if that is where it is mounted, or else it can be locked rigidly with respect to the incident beam collimator. These settings are diffractometer specific, but the user must choose between the two COLLIMATOR or ω CIRCLE options available in the message display panel before exiting from telescope adjustment mode.

VIEW MODE

Three viewing modes are available. The default view is an overall view of the whole diffractometer. The second view has an additional reduced image of the crystal in the lower left corner, as seen through the telescope. The third view is a larger view of the crystal through the telescope. Note that the telescope view has greatly reduced functionality over the default diffractometer view.

DIFF TYPE

Currently has no functionality

PRIM VECTOR

Currently has no functionality.

SCAT VECTOR

SCAT VECTOR is a three state button for displaying scattering vectors of reflections lying on or near the Ewald sphere surface. In the first mode, only those reflections lying in the equatorial plane of the diffractometer are displayed, whereas in the second mode all reflections on the surface of the Ewald sphere are represented by scattering vectors. In the third mode scattering vectors are switched off.

DIFF VECTOR

DIFF VECTOR is a three state button for displaying the diffracted beams scattered by crystal in its current orientation i.e. those reflections lying on or near the Ewald sphere surface. In the first mode, only those diffraction vectors of reflections lying in the equatorial plane of the diffractometer are displayed, whereas in the second mode all reflections on the surface of the Ewald sphere are represented. In the third mode diffraction vectors are switched off.

EWALD

EWALD is a three state button for displaying the currently active reflections lying near the surface of the EWALD sphere as reciprocal space points, rather than vectors. The first mode displays just those near active reflections in the equatorial plane, the second displays all reflections near the Ewald surface, and the third mode disables the reciprocal lattice point display. It is important to note that the tolerance for points being displayed on this surface is essentially +/- 1/2h, k or l, which is in fact very much higher than you could expect in a real experiment, so that many more reflections appear active than is actually the likely, given their distance from the sphere surface.

HKL LABEL

This is another three state control for switching on/off the labelling of reciprocal lattice points lying near the Ewald sphere surface.

LAMBDA

Currently has no functionality.

PSI SCAN

Currently has no functionality.

HKL DRIVE

Currently has no functionality.

COLLECT

Currently has no functionality.

NEW FACE

Currently has no functionality.

EDIT FACE

Currently has no functionality.

DELETE FACE

Currently has no functionality.

PRINT

Currently has no functionality.

EXIT

Terminates the current PREABS process immediately.

RMB ?

This controls the default functionality of the Right-Mouse-Button. By default this is set to ω but successive selections change it to χ, φ and back to ω. In any particular mode, rotations about the corresponding diffractometer axis are calculated by representing that particular axis circle as a sphere centred on the crystal and projecting forward out of the screen, but constrained to rotate about its axis. Any right-mouse-motion is mapped to rotations of this sphere about the axis in question.

Known shortcomings

  • Crystal image doesn't necessarily reflect the true orientation on the measurement diffractometer - which could be confusing.

  • Non closed crystal shapes can cause disturbing image views.

  • Much of the intended functionality has not been written yet.

File Assignments

  • Reads hkl data from the input archive file(s).

References

  • Busing, W.R. and Levy, H.A. 1967. Angle Calculations for 3- and 4- Circle X-ray and Neutron Diffractometers. Acta Cryst. 22, 457-464.

  • Tanaka, K. & Saito, Y. (1975). Acta Cryst. A 31, 841-845.