a) to have an image of your crystal mounted on the goniometer in
orientation, in which the axis of interest (6-fold) is perpendicular to
the beam. You should know the system well enough to relate the coordinate
system of the crystal on this image to the beam-gravity coordinate system.
b) you collect in this orientation diffracion image(s) sufficient for
c) index the lattice and chose hexagonal lattice and refine parameters
d) then you collect data set from the crystal so you can solve the
structure in this coordinate system. Because space group is polar, there
are always two non-equivalent choices for the coordinate system and you
cannot replace one with another.
The critical step is performed after (c) and depends on software -- I
describe here HKL2000. On the image oriented according to (a) check where
are the positive and negative values of hexagonal index (l index - use
zoom window). HKL2000 present the diffraction image of the detector from
the perspective of an incident beam. Therefore, you would need to
correlate positive and negative values of indices with the optical image
coordinate system from (a). Remember that optical axis (of the camera
imaging a crystal) may not be along the beam. The structure solution will
provide you with the direction of axis c.
> I'm interested in knowing how to figure out the relationship between the
unit cell contents and the crystal habit in these crystals (small
attachment, two roughly orthogonal views).
> Space group is P64 (enantiomeric) , and you can clearly see the
> six-fold. The question becomes how to determine which direction the
screw axis is going with respect to "top" and the "base" of the
> pyramidal crystals (right image) so I can gauge how/why the crystals
grow this way based on the cell contents.
> Thanks in advance.
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)