The MAIN User`s Guide

General information about the program

User`s Guide Table of Contents

MAIN can do many things, probably too many for a beginner. The point is that one can learn new things only one by one and not all together. Decide about a beginning. There are namely as many beginnings as there are cases. The path below is only a suggestion.

First get MAIN running.

• License policy
• Installation procedure

Learn to use "main_config" tools. The configuration setup is the same for model phases from molecular replacement or from experimental phases:

• Start with an elementary case 1 molecule in an asymmetric unit .
• Next move to a case with N molecules in one asymmetric unit. This is a tutorial for averaging and manipulation of several related molecules simultaneously.

After mastering 1 or N molecule case with something on the screen it is time to move on to the following chapters.

General chapters on major topics

• Use of MAIN config tools
• Map calculations
• Building a new structure
• 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.
• Topology and Parameter Files This knowledge helps anyone dealing with nonstandard amino acids. Interface to X-PLOR- CNS-like files is described as well.

Special chapters including complete tasks

• Dealing with several crystal forms is an advanced topic, which does require knowledge of MAIN programing language. Includes averaging, NCS refinement and can be in principle extended to unlimited number of crystal forms. If you are not a MAIN expert yet, ask for help.