MAIN User`s Guide

User`s Guide Table of Contents

1. Learn to use "main_config" tools.

The config tools configure working environment by creating a series of macros which connect and organize data and GUI features. Macros are used during a main session. Without working environment configured "MAIN" is an infant not really able to understand your wishes, unless you doit yourself by writing MAIN language .

Each MAIN working session should be run in a separated directory in order not to mess up the working environments. The working environment must be created before starting "MAIN" and it can be reconfigured anytime.

• Load pdb file is the most elementary case, where a single PDB file is loaded and its 3D presentation configured.
• 1 molecule in an asymmetric unit is the elementary case for crystal structure determination, where a atomic coordinates (PDB file) and diffraction data and their manipulation including 3D presentation are configured.
• N molecules in one asymmetric unit. extends the elementary case to the use Non-Crystallographic-Symmetry and multiple segments. It is a tutorial for averaging and manipulation of several related molecules simultaneously.
• Multiple crystal forms extends the use of NCS to multiple crystal forms, by implementing cross crystal form electron density averaging and refinement.

2. Learn to do specific tasks.

• Use of MAIN config tools
• Map calculations
• Building a new structure: automated
• Building a new structure: manually
• Model rebuilding
• Structure analysis and validation Quality of models should be monitored continuously. Bad models should not be built in the first place - however - they should never enter refinement.
• Crystallographic refinement
• Density modifications gives an overview of density modification methods in MAIN (solvent flattening, electron density averaging). Now that "main_config" tools encompass most of density modification approaches, this chapter is almost obsolete.
• A high throughput setup , which provides guidelines to setup non-interactive interface to MAIN. It can be a base for a script, which could be invoked by an extranal program, shell or pipeline.
• Topology and Parameter Files This knowledge helps anyone dealing with nonstandard amino acids. Interface to X-PLOR- CNS-like files is described as well. Using PURY interface, however, this interface has become of a minor relevance.

3. Learn more about special chapters including complete tasks