Volume 2 Chapter 4 Display Menus COLOUR RESIDUE AND COLOUR SYMM-OP

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COLOUR BOND

Function

Colour-by-BOND displays the current 3D structure, colour-coded according to bond type.

The colours used on X windows and Tektronix 4200 monitors are as follows:

white
single
red
double
green
triple
navy blue
quadruple
pale blue
aromatic
magenta
polymeric
yellow
delocalised
yellow-green
pi
dark grey
unknown

On devices that only support colours 0 to 7, the choice of colour may change depending on the combination of bond types that happen to be present in the current structure.

If the colour key is switched on, the assignment of colours is displayed.

Note

Sometimes you will notice a structure displayed in part or in full with the bond type "unknown" (grey or yellow, depending on terminal type).

This phenomenon probably provides the best possible illustration of the so-called "matching numbers" which are a vital component of QUEST3D's 3D searches, and which allow QUEST 3D searches to be so much more efficient and precise than corresponding GSTAT searches.

Briefly, the matching numbers simply store the correspondence between the atoms in "2D chemical diagram" and the atoms in the "3D crystallographic diagram".

Since bond types for the 3D connectivity are not stored in the database, software must use the matching numbers to locate the bond in the 2D diagram which corresponds to the required bond in the 3D in order to determine the bond type.

If it has not been possible for the matching software at the CCDC to uniquely identify any bonds/atoms in the 2D corresponding to any atoms/bonds in the 3D for a given entry, that entry is referred to as "not matched".

If it has only been possible for some of the atoms/bonds in the 2D and 3D to be correlated in a given entry, that entry is referred to as "partially matched". This happens most frequently when some of the atoms are disordered, or when the coordinates of a solvate molecule were not located/reported.

Entries for which all atoms and bonds correspond are referred to as "prefectly matched" (approximately 85% of the master database at the time of writing - October 1993).

Thus, with the aid of a comparison between the "colour-by-bond" 3D display and the 2D chemical diagram, it is easy to locate rapidly the disordered or missing parts of the 3D structure.

Related Commands

COLOUR RESIDUE, COLOUR SYMM-OP,COLOUR ELEMENT, COLOUR HIGHLIGHT, COLOUR MONO

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Volume 2 Chapter 4 Display Menus CONTROL EXIT.