A three-fold twin in B2₁

3/7: 'Solve' using P2₁

The SHELXD ins file written by XPREP needs a bit of manual editing. Firstly, the wavelength is wrong (this is a CuKα dataset) and the ZERR line has incorrect values. Although SHELXD can solve this structure without being told of the twinning, the success rate is higher if a TWIN matrix is given. Also, the success rate is dramatically improved when WEED is specified. With these changes we can safely reduce NTRY to 20. Lastly, a SEED instruction is added so that repeat runs on the same hardware give reproducible results. After editing, the ins file looks like this:

This SHELXD instructions file is downloadable using the following link:

9mj-shelxd.ins

The filename needs to be changed to 9mj.ins to work with the 9mj.hkl dataset. On running SHELXD, the following summary is written to the screen:

From the looks of it, the structure was solved well before the 20th try. In Mercury, it looks like this:

Aside from a few disconnected parts, this is not so bad. SHELXD has assigned a few of the atoms as oxygen (red) and the rest as carbon (grey). It is straightforward, if a bit tedious, to manually build this into twelve discrete molecules. To proceed, we do need a more complete model, but it does not have to be fully refined. That's just as well, because anisotropic refinement of this P2₁ model is not stable, even with an extensive battery of constraints and restraints. Indeed, it was refinement instability that prompted a closer look. Luckily, for its intended purpose here, an isotropic model without hydrogen atoms will suffice. Similarly, it won't matter if some of the atom types are wrong; it just needs to be good enough. A few cycles of model building/refinement gave the following, in which all non-hydrogen atoms have been left as carbon:

Since this tutorial is not intended to be an exercise in laborious model building, the above model is available for download, here:

9mj-good-enough.res

In part 4 we'll use this model to create a 'detwinned' dataset for diagnostic purposes.