Solving molecules

The objectives of the project are to provide the student the opportunity to (a) solve a small
molecule structure, compare/contrast it to the reported literature and place it within the context of “why” the researchers solved that structure, and (b) research a structure from the protein data bank. The project will be a current area of science that X-ray crystallography has played an important role, and you are required to cover the topic area in the style of an in-depth mini-review.

What you will need…
→ Olex2 (
→ Shelx (
→ Mercury (
→ Pymol ( and
→ Please note that you will need to “register” for these programs, mainly so that you can get them
for an academic use and not pay for them
→ A PDB ID and HKL structure factor file for the “unknowns” you will be exploring

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The Work
– You will be instructed on install conditions etc. (PC only…Mac is similar but the CD does not
use Mac) so that everything runs properly (in particular Olex/Shelx)
– You will be given X-ray data for a small molecule structure (and associated reference to the
paper describing the structure) and the PDB ID code for a macromolecule
– You will be required to “solve” the small molecule and refine it to a value close to that of the
reported values.
– For the macromolecule, you will be required to do “a bit of modelling”….examine the structure
in PyMol and generate at least one colour figure of the molecule with a white background for your paper.

The Paper
– Length is to be no more than 20 pages (numbered), double spaced
– To be written individually
– Appropriate referencing throughout (numbered or name/year style)
– Should be written in the style of a targeted review
– Separate the paper into the two parts, (a) small molecule and (b) macromolecule.
– In Part A, describe what you did, your results and compare them to the published paper in Acta
Crystallographica Section E. In Part B, discuss the macromolecule, its structure and refinement and place it into context (aka…why was it solved etc.) … review the literature 🙂

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