Introduction to menus (GENERAL)

Introduction

The WHAT IF commands can be divided in several categories. The general commands, those are the commands that are always active. Most of these are described in the introduction (chapters 1,2,3,5,6). The so-called hidden commands, those are un-documented, but nevertheless sometimes useful commands, will be described throughout this writeup where-ever needed.

Many commands however, are logically grouped in menus. The following is a list of some of the titles of chapters in this writeup that deal with one of the more frequently used menus.

Chapter 09  Surface area calculations (ACCESS)
Chapter 10  Water operations (WATER)
Chapter 11  Quality control (QUALTY)
Chapter 12  Hydrogen bonds (HBONDS)
Chapter 13  Contact analysis (ANACON)
Chapter 14  Building proteins (BUILD)
Chapter 15  Superimposing structures (SUPPOS)
Chapter 16  Van der Waals menu (SETVDW)
Chapter 17  NMR specific options (NMR)
Chapter 18  Families and clusters (CLUFAM)
Chapter 19  Data spread sheet (TABLES)
Chapter 21  Torsion angle evaluation and manipulation (CHIANG)
Chapter 23  Structure verification (CHECK)
Chapter 24  Hssp related commands (HSSP)
Chapter 27  Secondary structure (DSSP)
Chapter 29  Digitization of stereo images (DIGIT)
Chapter 31  Working with maps (MAP)
Chapter 35  Symmetry operations (SYMTRY)
Chapter 36  Amino acid structure regularization (REFINE)
Chapter 38  The electrostatics menu (ELECTR)
Chapter 40  The structure fragment database (DGLOOP)
Chapter 41  Relational protein structure database (SCAN3D)
Chapter 42  Selecting database proteins (SELECT)
Chapter 43  Atomic parameter correlation rows (SEARCH)
Chapter 45  3-dimensional structure superposition (3SSP)
Chapter 46  Sequence manipulation (WALIGN)
Chapter 51  Using the graphics (GRAFIC)
Chapter 52  Graphics objects and items (ITMADM)
Chapter 53  Two dimensional graphics (GRATWO)
Chapter 54  Graphics enhancement options (GRAEXT)
Chapter 55  Colouring atoms, residues, molecules, etc. (COLOUR)
Chapter 56  Plotting (PLOTIT)
Chapter 57  Labeling atoms (LABEL)
Chapter 58  Very fancy graphics; molecular pornography (PORNO)

These menus are logically grouped in a few categories:


Generally useful menus.
Menus mainly useful to crystallographers.
Menus that allow for access to databases.
Menus that mainly deal with graphics operations.

To go to a menu you have to type the name of that menu. These commands are general commands, and therefore you can always from every menu go to every other menu. Whenever you are in a certain menu, you can use the command END to leave that menu.

The first couple of exercises in the tutorial make the travel through the menus clear to you.

Pull-down menus

Pull-down menus have been implemented on all hardware platforms except DOS machines.

The following pull-down menu description therefore only holds for SG machines, but is highly likely to be valid for the other platforms too.

The menu bar at the top of the screen holds the names of WHAT IF menus. Pick one of them and a pull down menu with most of the commands that you expect in this menu will appear. Pick an option in this pull down menu, and a window will pop up. In this window you are directly in the option that you picked. You do not have to navigate through the WHAT IF menu maze first. The last line you see in this pop-up terminal window is often: Hit RETURN to continue. If you do hit return, the window disappears again.

If you pick HELP in the right most menu (right most column; the one that is alway there) the HELP option gets activated. If the HELP option is activated after you picked the the pull down menu box (that is green now), you will get SHORT help on all the commands in this menu. If the HELP option is activated, and you pick a box in the pull down menu, the terminal window will pop up, and extensive help about this option will be displayed.

Remember that the HELP option stays active till you pick HELP again.

Manipulating the pull down menus

There are many more pull down menus than can be visible at the same time. At this moment (1-3-94) there are some 50 pull down menus, but another 10 will be added this year. The arrow buttons -> and <- left and right of the pull-down menus can be used to shift through the pull down menus in the indicated direction.

The private menu

There are many pull down menus, and it often happens that you want to use commands from several menus in a row. To avoid excessive picking, a private pull-down menu has been added. This is the second menu from the right.

If you have a file called MY_MENU.DAT with at most 30 commands in it in the directory from where you started WHAT IF, than the private menu will hold these commands. Otherwise you get the generic private menu.