Volume 1 Chapter 13 Customising your QUEST/QUEST3D Implimentation

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14.1 Introduction

GSTAT is a multi-functional geometry program within the Cambridge Structural Database System (CSDS). It will perform:

Fragment location and geometrical calculations are of two types:

The GSTAT program uses two mandatory input files:

The GSTAT program will optionally generate a number of output files, principal among these are:

The GSTAT program is supplied with both the basic and graphics implementations of the CSDS. In the former case, GSTAT provides the sole ability to perform 3D substructure searches.

Within the graphics version, much of the functionality of GSTAT (except the ability to perform statistical analyses) has been transferred to the upgraded QUEST3D program. In this Version, the processes of statistical analysis and of data visualization, are being transferred to a new menu-driven and interactive program called VISTA.

All releases of GSTAT issued after October 1st 1992 are interfaced to the graphics Version QUEST3D program via the "Fragment" file generated by that program. This interface permits GSTAT to take advantage of the improved precision of 2D/3D substructure searches that is afforded by QUEST3D.

Volume 4 (Chapters 1 - 9) of the CSD System Documentation describe the functions of GSTAT and the structure of the alphanumeric "Instruction File" through which these functions are accessed.

A central part of Volume 4 is Chapter 9, which presents a definitive glossary of GSTAT keywords and qualifiers, arranged in keyword order.

The earlier Chapters 2 through 4 of Volume 4 describe the operation of individual sections of the program, together with the associated keyword subset and illustrations of program input and output. Chapters 5 through 8 deal with miscellaneous background information essential to a full understanding of the GSTAT program.

The remainder of this introduction presents brief summaries of the functionality of GSTAT and its mode of operation. The introduction is ordered according to the Chapter titles of Volume 4. Items in bold upper case font in Sections 14.2 - 14.4 below are the relevant major GSTAT keywords.

14.2 Geometry Calculations for Complete CSD Entries (Volume 4 : Chapter 2)

Chapter 2 of Volume 4 describes the instructions required for calculations involving the complete crystal chemical unit, consisting of discrete bonded units or 'residues'. Functions available are:

Chapter 2 of Volume 4 also describes how the user may control (a) which entries are processed, (b) which elements are treated in the calculations, and (c) the content and layout of the results file.

14.3 14.3 3D Search and Geometry Calculations for Substructural Fragments (Volume 4 : Chapter 3)

Chapter 3 of Volume 4 describes the facilities for 3D search and for the calculation of molecular geometry for intramolecular and intermolecular chemical fragments. These comprise:

Later sections of Chapter 3 of Volume 4 describe how to control (a) the CSD entries to be used in these calculations, and (b) the content and layout of the results file.

Special and more detailed sections discuss the facilities available for (a) treating fragments that may exist in 'chiral' and 'achiral' chemical environments, and (b) handling the effects of topological symmetry that may occur in some simple chemical fragments.

The processes described in Chapter 3 of Volume 4 result in the generation of a data matrix of Nf rows and Np columns, where Nf is the number of fragments that are located and which pass the 3D selection procedures, and Np is the (fixed) number of numerical parameters specified for each fragment.

14.4 Visual, Statistical and Numerical Analysis of Fragment Geometry (Volume 4 : Chapter 4)

Chapter 4 of Volume 4 is primarily concerned with the analysis of the data matrix generated using the procedures described in Chapter 3 (Volume 4). Analyses may use one (univariate), two (bivariate) or many (multivariate) columns of the stored matrix to derive systematic results concerning the chemical fragment. Current GSTAT facilities are:

Chapter 4 of Volume 4 is NOT intended as a textbook on statistical and numerical methods. It does, however, contain many references to suitable background texts, and also to the application of statistical and numerical techniques to crystallographic data retrieved from the CSD.

14.5 Searchable Connectivity Representations in GSTAT (Volume 4 : Chapter 5)

Substructure search facilities within GSTAT operate on a distance-based crystallographic connectivity representation. Distance-based connectivity for the bonded residues of the crystal chemical unit is established using a set of 'standard' covalent radii during the building of each CSD entry. Details of this intramolecular connectivity representation are included in each FDAT entry and will be used as a default by GSTAT.

GSTAT has the ability to override this default so as to construct a distance-based intramolecular connectivity table which uses covalent radii that are input by the user.

GSTAT also has the ability to construct an intermolecular connectivity representation using van der Waals radii for specific elements that are input by the user. This intermolecular connectivity can then be used to locate fragments that involve hydrogen-bonded and non-bonded interactions between specified elements.

Chapter 5 of Volume 4 describes how to modify the connectivity representations that are used by GSTAT in the location of chemical fragments. It also describes the differences that exist between the crystallographic connectivity tables employed in GSTAT, and the chemical connectivity tables that are used by the CSD programs QUEST (basic) and QUEST3D (graphics).

14.6 Ordering of GSTAT Instructions (Volume 4 : Chapter 6)

The various functions that may be performed by program GSTAT lead, inevitably, to a large number of possible instructions. Chapter 6 of Volume 4 breaks these instructions down into subsets that are related to broad areas of GSTAT operations. It indicates any rules that govern the ordering of these subsets within the complete instruction set and, in some cases, the required ordering of individual keywords within a given subset.

14.7 The QUEST3D-GSTAT link (Volume 4 : Chapter 7)

The integration of 2D and 3D substructural searching within the graphics search program QUEST3D represents a fundamental advance for the CSD System. Specifically, it provides absolute precision in the identification of the constituent atoms of a substructural fragment, in terms of both the 2D chemical constraints and the 3D geometrical constraints that must be satisfied. This precision is not always available in the search mechanisms of GSTAT, as summarized in Section 14.5..

The QUEST3D-GSTAT link described in Chapter 7 of Volume 4 provides a mechanism through which GSTAT may take advantage of the integrated fragment location algorithms of QUEST3D. By this means, the fragment search mechanisms of GSTAT are circumvented, and the program will operate on the atoms identified in the more precise QUEST3D search.

14.8 GSTAT Output Files (Volume 4 : Chapter 8)

Chapter 8 of Volume 4 describes the information content and format of the various files that can be output by the GSTAT program.

These files consist of (a) files of atomic coordinates, (b) files of fragment geometry (the data matrix referred to in Sections 14.3 and 14.4), and (c) various files that are specific to one or more of the statistical and numerical techniques summarized in Section 14.4.

14.9 Glossary of GSTAT Instructions (Volume 4 : Chapter 9)

Chapter 9 of Volume 4 is the core of the GSTAT manual. It provides fully detailed definitions of each of the keywords, subkeywords and numerical values that can be input as part of a GSTAT instruction file.

The glossary is ordered alphabetically by keyword for ease of reference.

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Volume 1 Chapter 15 Introduction to PLUTO.