Dear MAIN user,
This manual will explain both how to use MAIN as it comes to you, and also how to tailor it to your needs and style, but it will not teach you crystallography although it will help you to gain some experience. MAIN is a very powerful program and a programming language which provides tools in the form of macros to diagnose many of your crystallographical problems. As you learn MAIN, try to develop the habit that before doing a task, you think first how you would do it (which steps should be taken) and then start clicking some items and maybe tackle the syntax and command macros. This will help you a lot to understand how MAIN is performing and what it is capable of doing.
Accept MAIN as a friend, with its own personality, affections, needs and logic, and it will treat you well and you will be happy with it.
Manual is organized in 3 parts: "User's Guide" (users_guide.html), "Depp pages" (dialog_manual.html) and "Command Reference Manual (ref_manual.html). You should read the "User's Guide first. It is organized in chapters, that cover a particular topic. Each chapter is self-sufficient and dedicated to master the particular task described therein. The power of MAIN lies in its flexibility and generality. The importance of MAIN interface as a programming language is decreasing as the MAIN tools gain more and more independance - they are getting automated. Anyway, the more chapters you will master, the more flexible MAIN will become under your fingers as you enter successive fields of macromolecular crystallography. Advisable start is the 1 molecule case (1mol/1mol.html). So, please, go ahead.
The part "Depp pages" is to be read next. This tiny piece of text explains how to use the mouse, keyboard and dials and what you can do with them, when running MAIN in its dialog mode. Remember that using keyboard is the most intuitive and flexible way of communicating with a computer. You can browse through the descriptions of the menu items by clicking them, when the documentation mode is turned on. Pressing 'h' in the image window toggles ON or OFF the DOCUMENTATION mode.
The third part "Command Reference Manual" gives you complete power over MAIN on the command language level. By knowing the MAIN language you are not only able to change arguments and variable values but also to write your own tools. "?" anywhere on the command line in a place of an unknown command word gives you the list of possible continuing commands. The word "HELP" typed in a place of a command word can bring you information from the "Command Reference Manual" files to the screen while running MAIN.
"Keyword index" (keyword_index.html) is an utility, which may help you to quickly find things you are looking for in MAIN manuals.
Quite a substantial part of MAIN runs through command file macros, so it is very important for you to be able to configure them them by using "main_config" utilities and maybe a text editor. You will then be able to use the menus to your own best advantage.
Do not hesitate to contact me in a case of any trouble. There is an anonymous FTP account available at stef.ijs.si (ftp://stef.ijs.si/) where you can any time retrieve the latest MAIN documentation, utilities, data files and a DEMO version. Licensed executable files will be put there on a request. MAIN the most frequently updated home URL is at html://www-bmb.ijs.si/.
dusan turk
Dusan Turk Department of Biochemistry and Molecular Biology JOZEF STEFAN INSTITUTE Jamova 39, 1000 Ljubljana, Slovenia
phone +386 1 477 3857 / 3802 / 3610 fax: +386 1 257 3594 E-mail: dusan.turk@ijs.si
MAIN development was and still is inspired via communications with MAIN users and other crystallographers all over the world. I wish to thank all MAIN fans and other users who helped me to decide what to do. However, there are a few persons and groups, for who I feel that explicit acknowledgments are mandatory.
As first, without doubt the most enthusiastic MAIN fan, Hans Brandstetter.
I am grateful to all members of Rober Huber's group in Martinsried, who were and are still the major group confronted with the fresh outcoming MAIN releases and bugs therein. In particular I wish to mention Peter Hof, Lars Prade, Tarmo Plom, Manuel Than and Tim Mather (who gave the friendly spirit to the greetings page.)
Similarly, my coworkers in Ljubljana are acknowledged too. They have to deal with fatal bugs, sometimes introduced on a daily basis. Gregor Guncar, in particular, deserves his name to be mentioned.
Lynn Ten Eyck is gratefully acknowledged for providing his FFT routines.
Saulius Grazulis is acknowledged for creating the first Perl script generating the "html" version of MAIN "Keyword Index".
Sasha Urzhumtsev and his crew from Nancy (Pavel Afonine, Andrej Fokine) are acknowledged for their help with the bulk solvent correction procedure . and incorporation of their target functions based on maximum likelihood for refinement and map calculations into MAIN in November 2002.
Jan Loewe compiled the first Mac (OSX) version of MAIN.
When refining or minimizing protein or nucleic acids models please cite: