International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 24.3, p. 666
Section 24.3.3.8. Use of the CSD software system: an example
a
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England |
The preceding sections can only give a flavour of the extensive search, analysis and visualization capabilities of Quest3D, ConQuest, Vista and Pluto, which are fully documented in manuals available online via the web address given below, or in printed form from the CCDC.
In this section, we illustrate the application of the CSD system to one specific example: a CSD-based analysis to examine the O—H···O hydrogen-bonding ability of the keto oxygen of Fig. 24.3.3.2. This example illustrates a number of key features of the software system. The example is constructed in terms of Quest3D terminology, but identical facilities are available in the ConQuest program.
Searches can be performed interactively or allowed to run to completion without further intervention from the user. In interactive mode, Quest3D presents each hit as it is located, as illustrated in Fig. 24.3.3.3, and can then display the 1D bibliographic information, a 2D structural diagram, the 3D molecular structure, or a 3D packing diagram by toggling between display options. For an intermolecular search, as exemplified here, the non-bonded contact that triggered the hit is clearly identified. For the example described above, a file of the four user-defined geometrical parameters (DOH, AH, THETA, PHI) for each hit is created for use by Vista.
Vista displays the geometrical parameters in the form of an interactive spreadsheet; the user may include or exclude specific substructures on the basis of numerical criteria during the data analysis, e.g. to focus on a specific range of DOH values, exclude outlying observations etc. Hyperlinking between Vista and the master CSD file means that all of the database information of Fig. 24.3.1.1 is immediately available during a Vista session, either by clicking on a particular fragment in the spreadsheet or on a particular data point in a histogram or scattergram. Use of Vista is illustrated for the >C=O···H—O example in Figs. 24.3.3.4, 24.3.3.5 and 24.3.3.6.
References
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc. Perkin Trans. 2, pp. S1–S19.Google Scholar