Prequest: 2.13 Paste 2D

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2.14 Make 2D

A very powerful feature for automatically creating the 2D chemical diagram and the chemical formula from the current display of the 3D structure.

PreQuest automatically assigns chemical bond types according to CSD standard practices (e.g. all nitro groups will be coded the same way). Each chemically discrete bonded molecule is taken separately and a search for the minimum overlap view is performed. The molecules are then arranged in a vertical stacked manner. The diagrams may be simplified by use of the CSD standard group symbols e.g. Ph for phenyl (see Vol III. Appendix 8 and Section 2.16).

The process is highly successful for organic compounds and will even work in the complete or partial absence of hydrogen atoms. There may be occasional ambiguities, and some metal complexes and delocalised-charge systems are known to give problems, so these should always be visually checked in the 2D window.

If the diagram is not acceptable it can be edited using 2D Edit.

Important Note

It is hoped that most users will find the 2D diagrams acceptable for their private database. However, it is important to realise that this chemical connectivity is vital to the sub-structural search procedures in Quest. The bond types and charges will be exactly as you provide them. Any 3D search in Quest requires that a hit is first made on the 2D diagram.

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PreQuest: 2.15 1D Edit .