QUANTA/X-Ray Building Tools: Overview

Introduction

The aim of these five tutorials is to allow you to use the X-ray applications on real data to get an idea of what can be done. There are two datasets to edit:

1. The first contains no coordinates and consists of three maps: the first of these maps represents the exact data used in 1987 to solve the protein structure; the second is the same data but density-modified; and the third map is an artificially degraded map, where the phases are generated using only one derivative to give an SIR map. You will be using this data for the secondary structure detection and with the C-tracing X-POWERFIT application.
2. A partially refined insulin structure at 2Å. You will use this data and partially built model for the remaining 4 tutorials to practice the basic functionallity of the application, model building, adding solvent, and finally, adding a ligand.

Although QUANTA also provides an interface to X-PLOR, this is not covered within these tutorials.

Thank you to Dr .Jean Whittingham from the Protein Structure Research Group, Department of Chemistry, University of York, England, for providing the partially refined insulin structure and data.

1.) Getting Started

The first tutorial assumes you have no previous knowledge of the use of QUANTA and so gives you 30 minutes to practice manipulation of the display and positioning of the main view.

2) X-BUILD Tutorial

The X-BUILD tutorial involves general model building of a partially refined insulin structure. The examples in this tutorial include using the grid, gradient and torsion angle refinement tools to carry out the model building. The use of the interactive regularizer will also be used to model sections of the insulin structure.

3) X-POWERFIT Tutorial

The X-Powerfit Tutorial involves the analysis and interpretation of three electron density maps of the protein RNAse, solved in 1987. The tutorial also shows methods to refine secondary structure into electron density, and an extension to the semi-automated fitting tools to automatically trace multiple residues into density.

4) X-LIGAND Tutorial

The X-LIGAND tutorial is very short, and involves fitting a small ligand (methylparabenzene) to the partially refined insulin structure. This example only has 2 internal degrees of freedom, but demonstrates the principles behind the fitting application. This tutorial should take no more than 10 minutes to complete.

5) X-SOLVATE Tutorial

The X-SOLVATE tutorial is a very short tutorial which involves the fitting of water molecules to the partially refined insulin structure. This tutorial should also take no more than 10 minutes to complete.