Rigaku School for Practical Crystallography: Applications of software, techniques and technologies
June 24, 2021
I’m a Research and Applications Scientist on the Materials Science team at CCDC, and I recently taught a session at the Rigaku School for Practical Crystallography, which ran from June 7–18, 2021. The school focused on practical applications of software, techniques and technologies for crystallography. This blog contains links to my recorded modules as well as a self-assessment quiz you can use to check what you’ve learned.
Introduction to the CSD
My session at the school covered three main areas: how to search the CSD using ConQuest, how to work with molecules in CCDC’s Mercury software and how to deposit structures in the CSD. The complete playlist is available here, or you can watch individual modules below.
Module 1: Searching the CSD with ConQuest
The CSD is the world’s only fully curated and enhanced database for small-molecule organic and metal-organic crystal structures, and it contains over one million entries from x-ray and neutron diffraction analyses. Each crystal structure undergoes extensive validation by expert chemists and crystallographers – so extremely high-quality data is available. Entriesare also enriched with bibliographic, chemical and physical property information to add further value to the raw structural data.
In Module 1, I walk through ConQuest, which:
Enables search and retrieval of information from the CSD.
Provides a full range of text and numeric database search options.
It also enables, chemical substructure searching, 3D geometrical searching and intermolecular non-bonded contact searching. Click play to learn more.
Module 2: Working with Molecules in Mercury
Mercury uses the unique data in the CSD as a knowledge base for identifying likely molecular conformations and intermolecular interaction modes. In particular, it enables you to:
Generate conformers based on geometrical statistics from the CSD.
Map interaction preferences around complete molecules in a crystal structure.
In Module 2, I walk through practical tips for using Mercury, including how to:
Output ray-tracing images, print3D models, plot ellipsoids, export video and use the polyhedral display for large metal-containing structures.
Access the structure information panel, which can contain data from a CIF or a CSD entry.
Visualize hydrogen bonds and extended hydrogen-bond networks.
Color disordered parts, or “suppressions” as it is called in Mercury.
Automatically label stereocenters for all assigned bond types, which demonstrates chirality.
Pack structures to grow unit cells using the packing and slicing interface.
Overlap molecules from an asymmetric unit cell to compare conformations.
Click play to cover these topics and more.
Module 3: Depositing Structures to the CSD
The CCDC accepts depositions of crystal structure data in CIF format from single-crystal and powder studies and from x-ray, neutron or electron diffraction for organic compounds, metal-organic compounds and inorganic compounds. Our deposition services aim to make it easy for you to follow community recommendations and provide reliable data and metadata.
In Module 3, I cover:
When and why you should deposit your structures.
The steps in the deposition process.
After watching the videos, try this self-assessment to see what you’ve learned!
Read more about how Mercury supports the investigation and analysis of crystal structures.
Read more about how to deposit structures.
Do you want to learn on-demand how to use the CSD and get a certificate? Try CSDU.
CSD 3D Print (3)
CSD Conformer Generator (4)
CSD Python API (12)