Tips and Tricks in Crystallography
Mohana Rao (NCI): "Headache"
Medicines. The X-ray data
are collected, indexed, and processed. The R-merge is good. But
still one feels a bit queasy about it. Two cell dimensions are
close and the angles seem to be funny. Maybe the crystal system
chosen by Denzo is not the right one. Maybe there is a centering
somewhere. I am presenting a simple way to study these. During the
last week or two, I had the chance to discuss at length issues
like these not once but twice. The first thing I did was to create
a coordinate file (WH type) that has lattice points from -3 to +3
in all directions. Then these were converted to a PDB file using
the (doubtful) cell dimensions. The lattice points were then
displayed using a program like Insight. A typical cell was
constructed by joining the various lattice points. Viewing this in
three dimensions and rotating it in all possible ways, it was
possible to obtain alternate cells- from one triclinic to another
triclinic cell in one case and from monoclinic to C-centered
orthorhombic in another case. In this way, not only the correct
choice of the unit cell may be made, but also how the whole thing
fits in three dimensions may be understood.
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