Insight II



4       Viewer Module

The Insight II program's most frequently used commands are in every module, grouped into the pulldowns listed in the top menu bar. These commands comprise the Insight II program core, and are collectively referred to as the Viewer module.

The lower menu bar includes pulldowns with application-specific commands restricted to certain modules. To access these pulldowns and commands, pick the Modules icon (the Biosym logo in the top corner of the screen), then select a module of interest.

Certain pulldowns and commands can be accessed by picking icons from the icon palette. The icons can provide quick access to pulldowns and commands from any module. By default, the icons are set to access primarily Viewer-module functionality. However, you can customize the icons to access any commands that you choose. Refer to the Icon information in Chapter 1, Introduction.


Implementation

Window Layouts

During the course of a session using the Insight II program it is common to create and interact with several application windows simultaneously. The main window and Spreadsheet windows are two examples. Since these windows are all independent windows you can manage your workstation screen space by raising, lowering, moving, resizing, and iconifying the windows with the window manager. However, it is often the case that several of the windows are related, and it may be convenient to be able to perform these window manager type activities on all of the windows at once.

The Insight II program provides this capability through the use of window layouts. A window layout is an abstraction which organizes a set of windows so that they can be raised, lowered, resized, moved, and iconified as a single unit. The layout consists of two parts: the layout template, and a list of windows to manage.

The layout template does not refer to specific windows, but rather contains a set of entries each of which describes the position of a window relative to the whole template. This position is described as the position of the left, right, top, and bottom edges of the window as a percentage of the entire layout size. For example, a layout template might specify a layout of three windows as shown below. The left (l), right (r), top (t), and bottom (b) values of each of the three entries are shown on the diagram.

As mentioned above, a layout also contains a list of application windows that are managed by the layout. As each application window is added to the layout it is placed in the position specified by the next available template entry. In the diagram above, the first window added to the layout would occupy the upper left position, the next window would be placed in the upper right, and the third window would go below the other two.

Note that since the order in which the windows occur in the layout determines which template entry is used, if a window is removed from the layout, the other windows rearrange so that no template entries are skipped. For example, if a layout contained three windows (w1, w2, w3) and the layout template above, then initially w1 would be in the location described by entry 1, w2 in entry 2, and w3 in entry3. If w2 were then removed from the layout, w3 would now be the second window in the layout, so it would move into the position specified by entry 2. Since the edges of each entry are given as percentages, they do not directly specify the actual size of the whole layout. To do so, one of the windows must be designated as the control window for the layout. The size and position of the layout are then computed based on the size and position of the control window. As this window is moved and resized, the rest of the windows are automatically updated to satisfy the layout template. By default, the first window in the layout is the control window. However, any window can be designated as the control window by using the Apply option of the Window/Layout command. By turning off the Use_Control_Window option in that command, you may choose not to use a control window, in which case the windows all move and resize independently. A special string (" - Controls layout NAME") is appended on the window name in the window title bar to identify the current control window.

To create a window layout you must first have some secondary windows to be managed by the layout. Then go to the Window/Layout command and select the Use_Template option. Enter a unique name for the Layout_Name parameter, and then choose an existing layout from the Layout_Templates value-aid to fill in the Layout_Template_Nam parameter. This defines the layout template to be used. Next select the Add_Window option, and choose a window from the Window_List value-aid to fill in the Window_Name parameter. Repeat this action once for each window to be managed by the layout. When you add the first window, the only change you should see is that the title bar of the window should change to indicate that it is the control window. As each of the other windows is added, the window size and location should change to fit the layout template.

To change the control window simply select the Apply option, turn Use_Control_Window on and select a new window.

There are a couple of default layout templates which are read in on system startup, but the most common way to use layouts is to create them yourself using window arrangements that you prefer. To define a new layout template, simply set up the windows in the desired sizes and locations using the window manager. Then add all of the windows to the layout as described above using a new layout name. Note that in this case you do not have to have a layout template defined for the layout. Then go to the Window/Layout_Template command, and select the Create option. Make sure that the Layout_Name is the name used when adding the windows, and enter a new, unique name for Layout_Template_Nam. This creates a new layout template with one entry for each of the windows in the layout.

You can then write this layout template out to a file so that it may be used again in the future. To do so, select the Put option, and enter a filename (you do not need to add the default extension of .ltpl). This, or any other layout template file may be read in with the Get option of the Window/Layout_Template command. If you want to use this layout template regularly, you may add it to the system layout template file described in the File Formats section, Appendix B.

Spreadsheet Introduction

The Insight II molecular modeling program includes an integrated spreadsheet. This can be used to view various properties of structures in a tabular form.

The Insight II program's spreadsheet is a fully functional spreadsheet with the ability to view textual and numerical data. The numerical data may be calculated and can be derived from formulas or from other data in the spreadsheet. The spreadsheet includes features such as cut and paste, dynamic calculation of arithmetic expressions and functions, references to cells, and data plotting. In addition, spreadsheets are integrated into the Insight II program environment in the following ways:

Figure 15 . Spreadsheet

 

Creating a Spreadsheet

Spreadsheets may be created in one of three ways:

1.   Use the New Spreadsheet command to create a blank spreadsheet, which may be edited to enter data. The spreadsheet appears in a separate window from the main window of the Insight II program, thus making it possible to arrange it on the screen independently of the main window (see the Window Layouts section for more information about managing windows).

2.   Use the Tabulate Molecule or Tabulate Trajectory command to produce a spreadsheet which contains data regarding the object under study. These commands offer various options which make it possible to select which properties are listed in the spreadsheet.

3.   Use the Open Spreadsheet command to import data from a text file. This makes it possible to bring data into a spreadsheet which was created by another program. The text option to this command specifies that columns within the text file are delimited by tab characters. The graph option to this command specifies that columns within the text file are delimited by space characters (the convention used by the Put Graph command).

Modifying the Spreadsheet Layout

Once a spreadsheet has been created, the appearance may be modified in a number of ways to tailor the appearance of the data within it. Among the display characteristics which may be modified with the commands of the Format pulldown are the colors of the cells, the numerical formatting and alignment of the data, and the display of cell borders.

Manipulating Spreadsheet Data

The data within a spreadsheet may be treated as a small database by the use of the Sort and Search commands. With the Sort command, you may order the rows of the spreadsheet based on the numerical data in a specified column. With the Search command, rows which meet certain criteria may be selected. In the case of a spreadsheet which was created with the Tabulate Molecule command, the atoms of the selected rows may then be used as input to subsequent commands which operate on atoms.

Displaying Spreadsheet Data

In addition to viewing the data within the spreadsheet in a tabular form, you may plot the data as graphs using the commands of the Plot menu or the command buttons at the bottom of the spreadsheet window.

Using the Spreadsheet

Spreadsheets have a number of associated commands which are accessed via the pulldown menus at the top of the spreadsheet window. In addition, there are a number of interactions which take place directly with the spreadsheet, such as selection with the mouse, data value editing, and command buttons. Summaries of each available command are provided in the Command Summary section later in this chapter.

Selection
Many spreadsheet commands operate on a cell. To specify a cell on which to operate, select the cell before issuing the command. Selection of a single cell is accomplished by clicking the mouse button on the cell. A bold outline around the cell is displayed to highlight the selected cell.

Most spreadsheet commands can operate on multiple cells. Selection of multiple cells can be performed in a number of ways. The simplest is to click and drag over a rectangular area of the spreadsheet: this selects the cells within the rectangle. These are displayed with a black background to indicate they are selected. A selection may be extended to a larger rectangle by clicking the mouse button while holding down the shift key. This extends the current selection to the newly selected cell. A discontiguous selection may be created by clicking/dragging over a region while holding down the control key. In this case the current selection remains, and an additional selection region is created. Entire rows or columns may be selected by clicking on the row or column header.

Data Value Editing

Expressions

Data values may be entered into cells by creating a spreadsheet with the Tabulate commands or by importing a text file, but it is often useful to interactively edit the values by typing in strings, numbers, arithmetic expressions, and formulas. These data values may be literal, in which case the text which is typed in is displayed in the cell, or they may be an expression which is calculated, in which case the results of the calculation are displayed in the cell.

To enter a data value, select the cell to be edited as described above, then type in the data value while the mouse is in the window of the spreadsheet to be edited. The text is displayed in the text widget near the top of the window as you type it in.

To enter an expression, type in an equal sign (=) as the first character. The expression may consist of numbers, cell references, or formulas. These may be combined with the following arithmetic operators: +(addition), -(subtraction), /(division), *(multiplication), %(modulus), and ^(power). Parentheses may be used to logically group subexpressions.

Numbers may be entered literally, either as integers or floating-point numbers. Cell references may be entered by typing in the column letter followed by the row number, for example B6, or by clicking on the cell to be referenced. Formulas may be used in expressions to concisely use complex calculations within an expression.

Formulas

Formulas are indicated by entering the name of the formula followed by the input value(s), delimited by parentheses. Here is an example of an expression which uses a number, a cell reference, and a formula: = 2 + B6 + cos(45)

Formulas come in five categories: trigonometric, general math, tables, molecule geometry, and user-defined.

The trigonometric formulas take a single input value and include the following: cos, sin, tab, asin, acos, atan, sinh, cosh, tanh. The units are degrees. The constants PI, DEGTORAD, and RADTODEG are provided for use with these formulas.

The general math formulas include: log (natural log), log10 (log, base 10), sqrt (square root), and abs (absolute value).

The table formulas include sum(a1..a3) to compute sums of cell values, and avg(a1..a3) to compute average cell values. For example, =avg(A1..A10) computes the average value of the column of cells from A1 to A10.

The molecule geometry formulas include dist(atom1, atom2), ang(atom1, atom2, atom3), and dihedral(atom1, atom2, atom3, atom4) to compute intramolecular distance, angle, and dihedral, respectively. The input to these formulas is atom specifications of the usual Insight II type. Surround each specification with double quotes. For example: =dist("CRN:1:CA","CRN:10:N"). Note that the geometry values that are displayed in the spreadsheet by these formulas are automatically updated as the geometry of the molecule is modified by operations such as torsions and simulation animation.

User-defined formulas are formulas which you create to augment those listed above. User-defined formulas are BCL macros (See the BCL chapter to learn how to write BCL macros). You create them like any other BCL macro and refer to them by name as if they were any other formula. Currently, user-defined macros must return a value of the type "float".

Cell References
Expressions may contain references to other cells, in which case the reference is replaced by the value of the referenced cell at the time it is calculated. Cell references may be entered by typing in the column letter followed by the row number, for example B6, or by clicking on the cell to be referenced. By default, references are relative to the current cell. If rows or columns are inserted, the reference is updated to reflect the addition or deletion of rows or columns. If you wish a reference to be constant, that is, have it remain unchanged when cells are moved, precede the row, column, or both, by a dollar sign ($). For example: = 2 * $B$6


Command Summary

The top menu bar consists of pulldowns which access the core commands. The pulldowns are Module, Session, File, Object, Molecule, Measure, Transform, Subset, Assembly, User, Spectrum, Custom, Window, and Help In addition, this section contains summaries of the commands available when you pick the Contour icon, and the Spreadsheet icon, including the commands available only within the Spreadsheet window.

Module Pulldown (MSI logo icon)

The Module pulldown contains commands that you use to switch from one module to another. This pulldown is accessed by picking the Biosym logo in the top corner of the Insight II program's window, and contains the names of available modules. The contents of this pulldown depend on the software configuration at your particular site.

With the exceptions of Discipline and Licenses, selecting any of the commands in this pulldown causes additional pulldowns containing the commands which are specific to that module to be added to the lower of the two menu bars.

Builder

The Builder command activates the Builder module. This module allows you to construct new molecules from molecular fragments or individual atoms. It also allows you to modify such properties as atom type, hybridization, potential function parameters, bond order, and geometry of existing molecules. You can use the newly created or modified molecules in all of the normal ways throughout Insight II.

Biopolymer

The Biopolymer command activates the Biopolymer module. The commands in this module facilitate the building and modification of peptides and proteins. In particular these commands can be used to: build up peptide sequences while imposing secondary structure, delete or replace residues in peptides and proteins, impose secondary structure on existing peptides and proteins, and change N and C terminal capping groups. Other commands in this module allow you to search a database for, and display regions of, proteins which meet a given geometric criterion. This module includes access to many of the commands from the Builder module, allowing you to perform builder functionality while in the Biopolymer module.

Activity_Prediction

The Activity_Prediction module is used to identify biophores within small molecules of known activity. This module may also be used to predict the activity of novel compounds of interest. The activity prediction and biophore identification is done by analyzing molecular descriptions such as heteroatoms, aromatic rings, pi-populations, hydrophobicity, formal charges, bond dipoles, electron donors and acceptors, and frontier orbital coefficients. Please refer to the Apex-3D User Guide for a complete description of this functionality.

DelPhi

The DelPhi module has commands to define the DelPhi calculation parameters (Setup), perform a DelPhi calculation (Launch), analyze the results (Potential), and create charge and radius templates (Templates). DelPhi itself is a software package which calculates the electrostatic potential in and around macro-molecules, using a finite difference solution to the Poisson-Boltzmann equation. The program allows specification of ionic strength as well as dielectric constants of both the solvent and the molecule of interest. In addition, periodic boundary conditions may be used for molecules or systems with repetitive portions, such as nucleic acids.

Solvation

The Solvation module has been implemented in order to simplify and speed up calculating the solvation energy using DelPhi. It involves one or two DelPhi runs (based on the parameter set--CFF91, PARSE, ESFF--used), a Discover run for calculating the intramolecular energy, and a calculation of the total accessible solvent area. In addition, this module provides several other simple solvation models. Finally, a separate option to calculate the total solvent accessible surface area, using current Insight II atomic radii, is also provided.

Discover

The Discover module provides an interface to the Discover program. The interface allows for the definition of minimization and dynamics calculations. You can perform simulations using various forms of constraints and restraints, including template forcing, torsion forcing, tethering, and NOE. This module also enables you to do free energy calculations, and provides options for querying ongoing jobs.

Discover_3

The Discover_3 module provides an interface to the Discover 3.0 program by enabling you to specify molecular mechanics simulations using that program. It also provides basic options for querying ongoing jobs. The interface allows for the definition of minimization and dynamics calculations.

Docking

The Docking module provides facilities for calculating the nonbond energy between two molecules using explicit van der Waals energy, explicit electrostatic (Coulombic) energy, or the combination of van der Waals and electrostatic energies. The number of atoms included in the calculation can be limited by specifying a monomer- or residue-based cutoff. Alternatively, the computation can be done approximately, using a precomputed energy grid.

Ligand_Design

The Ligand_Design module provides functionality to help you design candidate ligands.

Search_Compare

The Search_Compare module provides functionality for calculating molecular volumes, performing boolean volumetric operations, and for performing systematic conformational searches.

CHARMm

The CHARMm module provides an interface to the CHARMm program, from which you specify molecular mechanics simulations using that program. The interface allows for the definition of minimization and dynamics calculations.

MBOND

The MBOND module provides an interface to the MBOND program, allowing you to specify molecular mechanics simulations using that program. The interface allows for the definition of minimization and dynamics calculations.

Homology

The Homology module contains commands to help build a model of a protein given only its amino acid sequence and the three-dimensional structure of at least one other protein. Facilities are provided to find regions of structural conservation among related proteins, to align amino acid sequences, and to assign coordinates based on these alignments.

NMR_Refine

The NMR_Refine module is a structure determination module that uses data from Nuclear Magnetic Resonance (NOE restraints) to determine the structure of a molecule. The module includes IRMA (Iterative Relaxation Matrix Approach) to refine restraints, and DGII (Distance Geometry) and SA (Simulated Annealing in Discover) to help predict structure.

XSight

The Xsight module contains a comprehensive set of commands for performing all aspects of macromolecular crystallography.

Ampac/Mopac

The Ampac/Mopac module provides an interface to the public domain AMPAC and MOPAC programs, which provide a semi-empirical solution to electron configuration problems. These programs can be used to predict such properties as electron distribution and partial charges. They can also be used to optimize small molecule conformations, create contours showing electron configurations, and perform various other calculations. You can also run AMPAC and MOPAC from the operating system level.

DMol

The DMol module provides an interface to DMol, a local density functional quantum chemistry program. The module provides options for choosing the type of calculation (e.g., energy, minimization, frequency), setting input parameters, and determining output quantities from the DMol calculation. It also provides the capability to restart energy and/or minimization calculations from previous results, and to launch DMol jobs on remote hosts. Molecular orbital, density, and other volumetric output from DMol may be contoured and viewed from within this module.

Turbomole

The Turbomole module provides an interface to Turbomole, a local density functional quantum chemistry program.

Zindo

Zindo is comprehensive semi-empirical SCF/CI program. It has many options, offering RHF, UHF, UHFA, and ROHF SCF calculations; energy, geometry, and CI options; and EHT, CNDO, INDO, NDDO, and PPP methods.

QuanteMM

The QuanteMM command activates the QuanteMM module. This module combines functionalities of the quantum mechanical programs MOPAC, Turbomole, and DMol with the capabilities of the molecular mechanics program Discover to perform calculations where a molecule, described by a quantum mechanical method, is embedded into an environment described by a classical mechanical method.

Analysis

The Analysis module is used to perform molecular conformation analysis. This module provides functionality for analyzing the trajectory data output by the molecular mechanics program Discover (separately licensed from Biosym). This functionality may also be used to analyze conformational data produced by other molecular mechanics programs, or by any other method, provided the data is formatted in a file type recognizable by Insight II.

The analysis is performed by defining properties of interest, identifying the atoms that uniquely define the property, and then graphing those properties against each other. Four types of properties are available for analysis: total energy, time, distance (including point-plane), and periodic (angles, dihedral angles, and plane-plane angles).

DeCipher

The DeCipher command activates the DeCipher module, which is used to perform molecular conformation analysis. This module provides functionality for analyzing the configuration data output by the molecular mechanics program Discover, separately licensed from Biosym. This functionality may also be used to analyze conformational data produced by other molecular mechanics programs, or by any other method, provided the data is formatted in a file type recognizable by Insight II.

The analysis is performed by defining properties of interest, identifying the atoms that uniquely define the property, and then graphing or tabulating those properties against each other.

Licenses

The Licenses command lists all licenses that can be checked out or checked in interactively during the Insight II session. There are other licenses, such as License_Holder, that will be listed in your license file but cannot be explicitly checked out/in. These do not show up in this command.

Those licenses which are currently checked out are displayed as ON; all others are displayed as OFF. Since an Insight II license is required to run Insight II, and since other licenses are required to run certain modules within Insight II, you may be unable to check back in a license. If so, you are notified in the Information window.

Also note that licenses are checked out automatically as you access parts of Insight II. You do not need to check in these licenses; they are automatically checked in when you Quit Insight II. But, you can check them in if you wish.

Bundles are special licenses which grant you access to the same software as would a set of individual licenses. They are used to simplify distribution of license files -- by reducing the number of lines in the average license file.

You can list the individual licenses (also called features) in a particular bundle by using the List_Features option of the License Action parameter.

For any license, whether you have it checked out or not, you can list the users of this license by using the List_Users option of the License Action parameter. This listing is not generated if the feature selected allows an unlimited number of simultaneous users.

Session Pulldown

The Session pulldown contains commands to customize the current Insight II session. Session commands also provide access to Insight II's comprehensive online help utility, allow you to exit temporarily or permanently to the operating system, and replay Insight II command scripts. Session commands, such as changing the background color of the graphics window, do not impact the contents of files created later using Save or Put.

Environment

The Environment command allows you to customize the environment of your current Insight II session. The features that you can control include the following:

Anti_alias in conjunction with the Antialiasing parameter enables or disables anti-aliasing. When Antialiasing is On, lines and curves appear smoother than when this feature is Off. However, when Antialiasing is On screen refreshes are somewhat slower.

RGB_Mode in conjunction with the RGBmode parameter allows you to change whether Insight II runs in colormap mode, or rgb mode. Each mode has advantages and disadvantages depending on which model of workstation you are using. Rgb mode generally allows more colors and higher quality cpks to be displayed, but may impact graphics performance. Colormap mode draws the fastest anti-aliased lines on most platforms but limits the number of simultaneously displayed colors. The default varies according to the model of your workstation.

Single_buffer in conjunction with the Singlebuffering parameter allows you to control whether Insight II runs in single or double buffer mode. Double buffer mode is the default. When in rgb mode on some eight-bit graphics board workstations such as the SGI Indigo, turning on single buffering improves the sharpness and detail of the image at the expense of the screen flashing during redraws.

Render_in_Motion in conjunction with the Render_Quality parameter allows control over how certain types of renderings such as CPKs, solid ribbons, and solid contours are drawn when they are being moved via the mouse or dials. When Render_Quality is set to Fast_Render various simplified representations are used to give faster drawing performance while in motion.

Subpixel in conjunction with the Subpixelposition parameter allows you to control whether subpixel positioning is used for points, lines, and polygons. Subpixel positioning causes points, line segment endpoints, and polygon vertices to be placed more accurately on the screen resulting in fewer artifacts and less jittering during movement. It is only effective when antialiasing is on and hence is meaningless on the eight-bit Personal Iris and G platforms. By default this parameter is set to Off.

Background in conjunction with the Background Color parameter allows you to change the color of the graphics window. By default, background color is BLACK.

Auto_World in conjunction with the Autoworlding parameter enables or disables the automatic addition of newly created objects to the WORLD assembly. The WORLD assembly is an internally-maintained assembly object that normally is the assemblage of all objects. It is used with such commands as Connect to allow you to rotate, translate, and scale all objects at once. If you do not want newly created objects added to the WORLD assembly, then turn this feature Off.

Default_CMD_Object in conjunction with the CMD Object Scope and Command Object parameters allows you to specify a default command object. Normally, when typing commands contained in pulldowns you must specify both the name of the command and the name of the pulldown. For example:

Typed: Get Molecule PDB pdb1crn.ent crn

where the name of the command is Get and the name of the pulldown is Molecule. However, you may specify a default pulldown. If, for example, Molecule is specified as the default pulldown, you could issue the command:

Typed: Get PDB pdb1crn.ent crn

and the word Molecule is implied by default. There are two kinds of defaults which may be specified. One that you can specify is a default pulldown on a per-module basis. For example, Molecule could be the default pulldown for the Viewer module, while Graph could be the default pulldown for the Analysis module. The other default that you can specify is a default global pulldown. A default global pulldown affects those modules that do not have a per-module default assigned.

Energy_Timeout in conjunction with the Energy Timeout parameter allows you to specify how frequently van der Waals overlap or non-bond energies are calculated in monitor mode. The default is every 0.1 seconds. A value of 0 has the effect of performing the calculation when the mouse button is released.

Random_Number_Seed in conjunction with the Seed Num parameter initializes the random number generators with the specified seed. This is particularly useful when log or restart files are used to reproduce a particular set of results or simulation.

Light_Source

The Light_Source command is used to set the apparent direction to the light source in an Insight II graphics window. The objects affected by lighting are mostly those drawn as filled polygons such as CPKs, solid ribbons, and solid contours.

This command allows interactive adjustment of the light source using the mouse. When the Light_Source command is active and the Direction To Light parameter selected, the inking cursor (a small pencil) replaces the normal pointer cursor indicating that inking is active. Moving the cursor out into the graphics area of the Insight II window and depressing the pick mouse button initiates interactive light source positioning. While the mouse button is held down a red circle is drawn indicating the extents of a virtual sphere upon which the light source position is set. Moving the mouse while holding the button down adjusts this position and updates the Direction To Light parameter accordingly. Moving outside the circle makes the K component of the Direction To Light zero, effectively placing the light source in the plane of the screen. The light cannot be positioned behind the object (K < 0.0) using the interactive interface.

Cmd_Display

The Cmd_Display command gives you control over the display of inactive parameters in the Insight II program's command parameter blocks. If you choose to show all parameters, then both active and inactive parameters are displayed in parameter blocks. Inactive parameters are displayed in gray and do not respond to user input.

If you choose not to show all parameters, then only active parameters are displayed. The parameter block adjusts its size to accommodate all the active parameters at any given time.

Use the Single_Column_CMDs parameter to control the display of parameters in commands with only one column of parameters. Use the Multi_Column_CMDs parameter to control the display of parameters in commands with more than one column of parameters.

Help

The Help command allows you to access the Insight II program's comprehensive on-line help facility. On-line help contains information on every Insight II module, pulldown, command, and parameter, as well as actual command examples. To access help, select the Help command in the Session pulldown, type the command help on the command line, or press the on-line help icon (the question mark button in the icon palette).

Parameters are available to specify at which level you wish to enter the help library.

Autosave

The Autosave command is used to control automatic saving of objects in the current Insight II session. When Insight II first comes up, automatic saving of objects is disabled. Autosave is used to turn on or off the feature and specify the interval between saves.

Backup

The Backup command is used to save objects to the Insight II session folder, insight_session.psv, located in the directory where Insight II was first started. A new file is created each time Backup is executed or the operation is invoked via the autosave mechanism.

Recover

The Recover command is used to restore objects from the folder created with the Backup command or the periodic autosave operation controlled by the Autosave command. Delete * is executed first.

History

The History command displays the commands in the current session's history buffer. By knowing the number of a command, you may recall it by preceding the number with an exclamation point. For example, !-7 recalls the seventh command counting from the last command that was executed.

Buffer

The Buffer command controls the number of commands stored in the current session's history buffer.

Alias

The Alias command in the Session pulldown allows you to create and delete aliases. An alias is a custom notation for a command. You can use an alias to give a command a more meaningful name, or to shorten a frequently typed command string. This command is used to create new aliases or to delete previously defined aliases.

Note that Alias remains active only at the token level. A valid alias token must be surrounded by white space, and it cannot be part of another token. For example:


>	alias create list 1,3,5

>	color ca:list green
In this case, the string "list" is not replaced with the alias value 1,3,5 because the string is part of another token.


>	alias create list ca:1,3,5

>	color list green
These commands color ca:1, ca:3, and ca:5 green because here "list" is a single token surrounded by white space.

Note that aliases may be used anywhere in a command as long as they are separated from the rest of the command with blanks.

Because alias token substitution applies to all command tokens, it is necessary to place a backslash (\) in front of the existing token in order to:

1. define an alias using an existing alias name.

2. use the alias name itself as a value, instead of the value represented by the alias.

For example, to create an alias named Exit, which is equivalent to the command Quit:


>	Alias Create Exit Quit
To redefine the alias token Exit, when the alias Exit already exists:


>	Alias Create \Exit Done
This command redefines the alias token Exit to have the value Done. If the backslash is not present, then the command:


>	Alias Create Exit Done
first replaces Exit with Quit, and then defines an alias Quit to be equivalent to Done.

A backslash is also required in order to use Exit as a value in a command:


>	Sample_command Sample_object \Exit
Here, the parameter value Exit is passed on to the command. If the backslash (\) is omitted, then the command:


>	Sample_command Sample_object Exit
results in the value Quit being passed in.

Button

The Button command is used to maintain the text associated with the buttons on the optional button box peripheral. It provides the ability to associate text with a button, clear the text associated with a button, and list the text associated with buttons. The text can be set to execute as a concurrent command. Once text is associated with a button, that text is output, exactly as if it had been typed, when the button is pressed. This makes buttons useful for holding frequently used commands or parameters.

Stereo

The Stereo command provides a stereo view of the object or objects in the graphics window. You are given the option of changing the stereo angle (the angle between the views) no matter what type of stereo is being utilized. There are two types of stereo available: Hardware Stereo and Software Stereo.

The Software Stereo command creates split stereo pairs, and you are required to cross your eyes slightly to see the stereo effect.

The Hardware Stereo command is intended for SGI systems equipped with special stereo hardware. If you have StereoView hardware, which utilizes an emitter and special glasses, then the environment variable STEREO_TRIGGER must be set. Users with Stereographics or Tektronix stereo hardware, with an external switch to change the monitor to stereo mode, should NOT define the STEREO_TRIGGER environment variable. The STEREO_TRIGGER variable is defined when the software is installed, but can be changed at any time.

Env_var

The Env_var command allows you to access environment variables from within the Insight II program.

Unix

The Unix command allows you to issue commands to the operating system without leaving the Insight II program. You can enter any valid UNIX command, including one that starts up a shell session. To exit a shell session and return to Insight II, type exit or press <control>-<D>. Changes to a subprocess, including to default directories and environment variables, do not affect the parent process.

Please note that although the Insight II program itself is not case-sensitive, UNIX is. You must type all operating system level commands that you invoke through the Insight II Unix command in the proper case.

Change_directory

The Change_directory command is used to change the default directory from which the Insight II program reads files, and to which it writes files.

Sleep

The Sleep command allows you to suspend the running of this program for a specified number of seconds. This is primarily useful when replaying a log file for demonstration/training purposes, allowing you to halt the display for a set length of time regardless of the processing speed of the host computer.

Quit

The Quit command ends the current Insight II session. This is the normal way to exit the program. Upon normal completion, the Insight II program names the logfile insight.log. Note that if the program terminates abnormally, it names the logfile WBLOGFILE.

File Pulldown

The File pulldown contains commands that allow you to perform operations on the contents of a file or folder. Folders are special files used by the Insight II program to store objects created during a session. Folders can contain multiple objects created during different Insight II sessions.

Save_Folder

The Save_Folder command adds object(s) to a folder. You can create a new folder, or insert an object(s) into an existing folder.

The comment parameter for the Save_Folder command allows you to specify a comment string that can provide information on an object stored in a folder. Both the List_Folder and Restore_Folder commands cause the display of this comment string to the textport. How the Insight II program handles duplicate object names can be specified.

Restore_Folder

The Restore_Folder command displays object(s) previously stored in a folder. Restore_Folder also displays the associated comment to the textport for each object it restores, if a comment exists. You can also use the Restore_Folder command to specify how the Insight II program handles duplicate object names.

Remove_Folder

The Remove_Folder command deletes object(s) from a folder.

List_Folder

The List_Folder command displays information on the contents of a folder to the textport. This information includes each object's name, date of last modification, and associated comment text. The List_Folder command is the only mechanism that queries the contents of a folder. Folders cannot be printed or edited with standard UNIX commands, such as more or vi.

Import

The Import command is used to read molecular data files into Insight II for viewing or analysis. Import is similar in function to Get, but adds features that permit searching for files utilizing an index and preview operations that make it possible for you to view the text or graphics contained in a file in a window separate from the main Insight II graphics window. The Import command utilizes different File_Filter strings for each file type that the command supports. File_Filter strings allow you to specify the file extensions that are to be accepted when a file list is created. Insight II provides reasonable defaults for these "filter_strings" but these defaults can be changed during the Insight II session to allow easy access to files with non-standard file extensions.

Export

Export is a companion command to the Import command. Molecular data within Insight II can be written in one of the available supported file formats.

Export_Plot

The Export_Plot command in the File pulldown allows you to write the present display to various output file types, including an intermediate plot file (.ipf), or directly to a specified hardcopy device.

When the input is directly from the screen all current transformations such as clipping and coloring are taken into account. The entire display is plotted except for hardware-created images such as CPK spheres and the variable linewidth of bonds.

To print hardware-created images such as solid contours, ribbons, and CPK'd molecules, use the Snapshot and Tops utilities provided by SGI, or the xpr and xwd utilities provided by IBM. See Chapter 7 of the Biosym Products System Guide for more information.

Export_Image

The Export_Image command allows you to capture a bitmap image (also called a raster image) from the current display and write it to a file, optionally sending it directly to a printer or previewer. To export images at 600 dots-per-inch (dpi) resolution you should have at least 128 MB of RAM, and note that a PostScript file saved at 600 dpi resolution may be as large as 200 MB. On an SGI workstation, Insight II should be running in OpenGL mode in order to export images at 300 or 600 dpi resolution. Otherwise text in the exported image may be clipped. Additional notes on using this command are provided online in the Biosym_xhelp system, accessed from within the Insight II user interface.

The captured image can be the entire graphics window, or a portion of it. The USER_DEFINED, NTSC, and PAL options for the Image Size parameter allow interactive specification of the region to capture.

Source_File

The Source_File command in the File pulldown executes a set of Insight II program commands from a disk file. You may use up to three nested levels of indirect files in any sequence of commands. This is particularly useful for repeated operations.

To terminate a sourcing process, press <Esc> on the keyboard. To temporarily halt the sourcing to review screen output, press <Backspace>. Then you can choose either <Esc> to exit the command, or press any other key to continue. Note that while the replay process is halted, you can use real or screen dials to rotate, translate, or scale the screen image. However, commands may not be executed.

Export_Molscript

The Export_Molscript command creates a molscript input file for each separate protein object (protein_id) in Insight II. The following options are available:

Minimum input for this command requires setting:

For each Molscript_file generated, a matching Mol__.pdb file is generated. Both files must be present in the same directory for molscript to work correctly. Postscript File options also generate a .ps PostScript file.

Note that MSI does not distribute the molscript executable. It must be properly installed and available in your PATH for the Postscript File and Show Postscript options to work correctly. Also, a properly installed PostScript viewer must be present for the Show Postscript option to work. Export_Molscript requires that the SGI_PS_VIEWER (on SGI) or IBM_PS_VIEWER (on IBM) environment variable be set to point to the postscript viewer. SGI_PS_VIEWER is set by default to xpsview and IBM_PS_VIEW does not have a default value.

Object Pulldown

The Object pulldown contains commands for manipulating objects.

For molecules, the object name is the first part of the molecule specification, which does not include the monomer/residue or atom specifications. As a result, the colon (:) character used in the full molecule specification is not allowed in an object name.

Also, most commands allow the use of wildcards in the object name to specify a set of objects. The wildcard character (?) matches any single character, and (*) matches any number of characters.

Copy Object

The Copy Object command creates a duplicate of the object you specify. If the object is a molecule or a user object, it makes an actual copy of all the vectors, atoms, and/or bonds. If the object is an assembly, it creates an assembly with exactly the same contents as the original assembly.

The newly created object may or may not be displaced from the original object depending on the value of the Displace parameter. Setting Displace to on helps you see the new object more clearly, since it is not coincident with the original.

Paste Object

The Paste Object command pastes an object from the Motif clipboard into Insight II. The clipboard may have been filled by an earlier Copy Object command with To_Clipboard set to On, or by a cut or copy operation using a compatible application running concurrently under the Motif window manager. A warning message is displayed if the Motif clipboard is empty or contains material with an unrecognizable format.

Currently, Motif clipboard operations are limited to 2D and 3D molecules and use MDL "mol" format. Compatible applications must use the "MDL_MOL" format identifier. When using the menus, Insight II fills in the New_Name parameter with the compound name from the "mol" format, if that is set. Otherwise you should fill in the New_Name parameter with a unique name for the new object.

Delete Object

The Delete Object command deletes a specified object. Once deleted, the object is removed from the screen, memory, and data storage. No memory of the object is retained.

Rename Object

The Rename Object command is used to give a new name to a specified object.

Blank Object

The Blank Object command is used to blank the display of an object. When an object is blanked, it does not appear on the display screen. In the case of molecules, the Blank Object command affects atoms, surfaces, CPKs, and ribbons.

Axes_Display Object

The Axes_Display Object command is used to control the display of the local and alternate axes systems for objects of any class.

Blink Object

The Blink Object command is used to cause an object to blink or flash on the screen. This facilitates seeing the minor differences between two objects which are very similar and which have been superimposed.

DepthCue Object

The DepthCue Object command activates or deactivates depth cueing for the specified object. Depth cueing aids in the three-dimensional perception of an object by drawing bonds and atoms which are farther away from the view point in dimmer colors.

LineWidth Object

The LineWidth Object command is used to set the width of the lines which are used to represent an object.

List Object

The List Object command lists general information about all types of objects. This listing includes the object name, the object type, and some specific information on the composition of the object. Information can be requested for all objects (the default), or for any single object. For more details on a particular object, you can use the List command which refers to the type of that object: List Assembly, List Molecule, List Contour, List User, List Graph.

Molecule Pulldown

The Molecule pulldown contains commands to manipulate molecules.

Get Molecule

The Get Molecule command brings a molecule into the working session.

Using this command, you can retrieve a stored molecule, which must be in one of these formats: Ampac, Mopac, Archive (Biosym .arc, .car, and .cor files are all read with the Archive option), Cambridge, free format, PDB (the Brookhaven Protein Databank data set), CHARMm, Quanta, MSF, or XPLOR. The default file type is Archive. If the file specified is a free format file, an additional file for reading that format must also be specified. The free format and Biosym-provided template files are described in Appendix B. HETATM cards may optionally be retrieved when reading a PDB format file.

You can also retrieve an entire archive file, or a single frame or range of frames from an archive file.

You may also specify a coordinate system for displaying the retrieved molecule relative to an already existing molecule.

Molecules are displayed using default values for Color, Bond_Order, DepthCueing, and Line_Width (see the Molecule/Set_Default command for setting the default values of these parameters).

When Insight II reads a file containing molecular data, it determines what element each atom is. This is crucial information for any subsequent operation on a molecule. The determination of element type is done by scanning the appropriate column in the input file. If an atom cannot be matched with a known element, an error is reported to the user. The elements known to Insight II are defined in the file elements.dat, located in the help directory. Insight II uses several different methods for establishing topology when molecules are read:

Sybyl Mol2 files and MDL molfiles and SDfiles
The connectivity information that is contained in the file is used explicitly.

Biosym car, arc, and cor files
An accompanying mdf file is also expected. The mdf file must have the same prefix as the car, arc, or cor file (e.g., test.car or test.mdf). If the mdf file is present, and refers to the same atoms as the car, arc, or cor file, the connectivity found in the mdf file is used explicitly.

Note that Insight II writes an informational message when the mdf file is being used. You should confirm the use of the mdf file by looking in the information area when reading car, arc, or cor files. If the mdf file does not match the car, arc, or cor file, or cannot be found, then a two-pass algorithm is used to establish the connectivity.

On the first pass the template file, amino_templates.dat, located in the $INSIGHT_DATA directory is checked for matches. The template file contains templates for amino acids including charged and terminal amino acids, nucleic acids, and a few commonly occurring residues and generic functional groups. A match occurs when a monomer or residue matches the name found in the template, has the same number of total atoms or heavy atoms only, and has the same atom names. When a match is found the connectivity for that residue is used from the template, with inter-residue connectivity being determined by distances and atom types. Each residue of a molecule is checked for a match, and those that have templates are assigned their connectivity from the templates. Any monomers or residues that do not match the templates have their connectivity established by distances. In the second pass bonding distances are read from the file elements.dat, also found in the $INSIGHT_DATA directory.

Any two atoms that are within the bonding distance plus a small margin of error are bonded together. If more than the appropriate number of atoms lie within bonding distance they are all bonded together. Insight II does not try to determine if any atoms close enough to be bonded should not be bonded.

You should note that you can add your own entries to the template file. For further information, refer to the Files section in the Utilities and Appendices volume of the Insight II Reference Guide.

Brookhaven files
The PDB Directory enum selects between reading files from the Brookhaven database as defined in $INSIGHT_PDB, and the current working directory. For complete information on reading in PDB files, refer to Appendix C.

The two-pass algorithm described above is used for establishing the connectivity in molecules read from Brookhaven formatted files. In addition the connectivity described by CONNECT records is also used.

AMPAC and MOPAC files
Connectivity is established by distances for AMPAC and MOPAC files, since they do not contain all the bonding information that is needed to completely define the connectivity of a molecule.

CSD Fdat
The two-pass algorithm described above is used for establishing the connectivity in molecules read from the Cambridge database.

Free Format Files
Free format files may contain explicit connectivity. In the cases that they do, it is used explicitly. Otherwise the two-pass method described above is used.

In the Insight II program, atom names are constrained to a five-character length.

Put Molecule

The Put Molecule command writes molecules from the working session into a disk file. The molecule may be stored in any of several formats: Biosym, Mopac (usable with Ampac or Mopac), free format, PDB, MDL, Sybyl-Mol2, CHARMm, or XPLOR. The default file type is Biosym. Files can also be saved in a format of your own specification.

Optionally, the Put Molecule command can be used to store only the atoms that are actually displayed, and store the molecule first applying the current transformation matrix to the molecule's coordinates.

Set_Defaults

The Set_Defaults command is used to view and set default parameters for all molecules which are brought into the working session by use of the Molecule/Get command. The parameters which may have defaults set using this command are Color, Bond_Order, DepthCueing, and Line_Width.

When the Insight II program is started, the default values of these parameters are retrieved from a file named .in2rc. The .in2rc file which is used is in one of three locations

1.   The user's local directory (the directory from which Insight II is run)

2.   The user's home directory

3.   The $INSIGHT_DATA directory (this file is on the Insight II CD-ROM delivered by Biosym and is not editable by the user).

The search order is as listed. If no such file is found in the local directory, Insight II looks next in the home directory, and so on. The $INSIGHT_DATA/.in2rc file is always present with the default values set at Biosym. The .in2rc file found at startup is the one used throughout the session.

The .in2rc files in the local and home directories are editable and can be updated by Insight II using the values selected in the Set_Defaults parameter block. You may also list the current default values at any time.

Parameter values are selected for each file type in the parameter block. You can set values for all file types at once by selecting All for the File Types parameter.

Choices for Coloring_Method are: By_Atom for coloring each atom according to its element type; Specified for coloring all atoms the selected color, for all subsequent molecules of that type; or Color_By_Rotation for coloring all atoms of the next molecule the selected color, and all atoms of subsequent molecules the next color from Insight II's color wheel.

Color Molecule

The Color Molecule command is used to render molecules and molecular attributes in color.

You can apply color assignments to only, or any combination of, sets of atoms in the molecule, ribbons, specified threads of ribbons, surfaces, or CPKs. Molecule, monomer, residue, or atom labels may also be colored separately. Colors can be specified by name or number, or by mixing a new color from a color palette. Colors can be assigned to individual atoms, by atom name, by atom charge, by hydrophobicity, or any specified property. Insight II can automatically select backbone, hydrogen, non-hydrogen, side-chain, or trace atoms.

Transparency Molecule

The Transparency Molecule command is used to adjust the degree of transparency effect used for the CPK, Ball_and_Stick, and Stick solid renderings of molecules. This is achieved by adjusting the alpha component of all colors in the spheres and cylinders used in the solid rendering of the specified molecule without affecting the r,g,b values (see Use of Color for more information). A Transparency Value of 0.0 means fully transparent and a Transparency Value of 1.0 means fully opaque.

Display Molecule

The Display Molecule command is used to turn on the display status of molecular attributes. This command is used to separately display atoms, residues, monomers, subsets, or molecules, as well as the axes, CPKs, ribbons, or surface attributes. Attributes can be selectively added to the display, or only specified portions of an attribute can be displayed. Backbone, hydrogens, heavy, side-chain, and trace atoms can be automatically selected.

Label Molecule

The Label Molecule command is used to create or remove labels for molecules, monomers, or atoms. A label is a short piece of text attached to a molecule, monomer, or atom. The text may be a property of the object it is attached to, such as its name or mass. Labels may be displayed with a variety of display characteristics, permitting display of the properties in a flexible manner.

Bond_Order Molecule

The Bond_Order Molecule command controls the display of multiple-order bonds. By default all bonds are displayed as if they were single bonds.

Surface Molecule

The Surface Molecule command is used to create and delete atomic dot surfaces. Three surface types are available: van der Waals, solvent (solvent accessible using the Connolly algorithm), and Quick, a pseudo-connolly surface that is not as precise as the SOLVENT method, but the calculation is much faster. The variables that can be controlled for the display are the number of dots per square angstrom, and whether the specified surface is to be displayed alone or added to the current display.

In the case of solvent accessible surfaces, the probe radius can also be varied.

The dot surface from a molecule can be written to a file using the Put option. The file format used is identical to that of the USER DOTS file, so the dot surface can be retrieved later as either a user object or as a dot surface on a molecule.

Render Molecule

The Render Molecule command allows you to control how the atoms and bonds of a molecule are represented. Available rendering styles are CPK, Ball_and_Stick, and Stick.

Ribbon Molecule

The Ribbon Molecule command is used to create or delete a ribbon representation of protein secondary structure. This command allows you to specify the number of strands to use in the ribbon representation, the offset distance to use in calculating ribbons around helixes, and the width of the ribbon (in angstroms). You can also, optionally, create decals to label the ribbons with residue property values

Color_Ribbon Molecule

The Color_Ribbon Molecule command allows you to color molecule backbone ribbons. A ribbon consists of a number of threads, and it spans one or more monomers. The smallest part of a ribbon which can be individually colored is a single thread within a single monomer.

SecondaryRender Molecule

The SecondaryRender Molecule command creates a Richardson style rendering of the secondary structure of a protein. The display parameters (e.g., size, color) for the rendering can be set with the Preferences parameter.

The SecondaryClassify Prostat command can be used to create a classification table for use by the SecondaryRender command. See the help for that command for more information about classification.

The SecondaryRender Molecule command works only on a whole molecule. If you need to create a display for a partial molecule, you can accomplish this by using Merge and Unmerge commands in the Modify pulldown in the Builder module.

List Molecule

The List Molecule command is used to display detailed information about specific molecules. You can list the names, coordinate information, charge group, potential type, atomic charge, fractional coordinates, minimum and maximum Cartesian coordinates, and link distances which match the molecular specification. The total energy of a molecule can also be listed if it has been previously computed or read in. The listed information may be displayed to the textport or to a specified file.

Tabulate Molecule

The Tabulate Molecule command is used to create a table that displays the molecular properties selected for the specified atoms. Each property is represented by a column of information, with the name of the property above each.

Browse Molecule

The Browse Molecule command creates a window which contains a table of molecules. This table can be used to quickly and easily browse through the molecules which are presently in the system. This browser offers the ability to blank or show molecules, connect molecules to dials, or select sets of molecules for use in subsequent commands, all with the click of a mouse.

 

Figure 16 . Molecule Browser

 

The browser is a table which lists the molecules and assemblies which are currently being modeled with the Insight II program. Each row contains four columns of information: the name of the object, the display status (On indicates it is currently displayed), and its dial connection status (Connected indicates that the object is currently connected to the dials).

You may use the browser to quickly change the display and dial connection status of objects. To change the display status, click on the table cell next to the name of the molecule or assembly. If it is currently on, your click changes it to off (and vice versa). The dials may be connected to an object by clicking in the Dials column next to the name of the object. You may connect the dials to world by clicking on the Connect World button. When connected to the world, this button changes to Reconnect to obj. Now this button permits you to connect back to the object which was connected before connecting to world.

The browser may also be used to select molecules for use with subsequent commands. Molecules are selected by clicking on their name in the browser. Selected molecules are indicated by yellow highlighting. More than one molecule may be selected at a time. To clear the selection so that no molecules are currently selected, press the Clear Selection button.

The selection may be used to easily operate on multiple molecules with the single execution of a command. For example, select a set of molecules which you would like to associate in an assembly. Choose the Associate Assembly command, fill in a name for the assembly, and press the Execute button. The selected molecules are now associated as members of an assembly with the specified name.

The browser also displays assemblies and shows the members of the assemblies, indented below the row which contains the assembly object. This may be used to quickly determine the contents of an assembly.

Molecules are added to the table automatically as they are added to the system, through commands such as Get Molecule and Append Residue, and are removed from the table when they are removed from the system using Delete Object.

Measure Pulldown

The Measure pulldown contains commands to measure certain fundamental quantities for molecules. Several of the commands also allow the setting of monitors. A monitor is a visual display of a quantity's current value, which changes dynamically as the objects involved move.

Quantities that can be measured include the distance between two atoms, the angle defined by three atoms, and the dihedral angle defined by four atoms.

The Measure command also provides a mechanism for measuring the internal energies of a molecule, including bond, angle, dihedral, nonbond, and cross terms.

Distance

The Distance command measures the distance between two atoms in the same or different molecules.

The output of the Distance command is determined by the Monitor parameter, which indicates whether the command uses distance monitors. A distance monitor is a visual display of the distance using a dashed line connecting the atoms, with the distance value above the line. The monitor changes dynamically as the atoms move. If Monitor is Off, the distance between the two atoms is reported in the information message area and the textport. You can also add, remove, or clear distance monitors, as well as display only distances between a specified minimum and maximum distance values.

Angle

The Angle command determines the current angle specified by any three atoms. The atoms do not need to be in the same molecule.

The output of the command depends on the value of the Monitor parameter. If Monitor is On, the dotted line between the atoms forming the angle and its measurement are displayed. If Monitor is Off, the three atoms, minimum and maximum angle, angle, and whether the condition criteria are currently satisfied are listed. The listing may be sent to a file or to the textport.

Dihedral

The Dihedral command determines the current dihedral angle between any four atoms. The atoms do not need to be in the same molecule.

The output for the Dihedral command is determined by the Monitor parameter. If this parameter is Off, the calculated angle, given in degrees, is reported to the information message area, as well as the textport. If the Monitor is set to On, the dihedral monitor is set up. This displays the dihedral angle by connecting the four atoms involved with dashed yellow lines, along with the current angle in degrees. You can also add, remove, or clear dihedral monitors, and specify values for the minimum and maximum dihedral angles to be monitored.

Monitor_Style

The Monitor_Style Measure command allows you to set the color of distance, angle, dihedral, bump, and hbond monitors created via the Distance, Angle, Dihedral, Bump, and HBond commands of the Monitor pulldown. In the Distance, Angle, and Dihedral flavors the color may be set for all monitors of a given type, or for specified monitors. In the Bump and HBond flavors all monitors of the given type are affected.

XYZ

This command determines the coordinates of an atom. The coordinates are reported in the information message area and the textport.

Bump

The Bump command is used to check for van der Waals overlap within a molecule or between two molecules. If overlap is detected, red vectors are drawn between the offending atoms and the distance between the atoms is listed.

Van der Waals overlap occurs when the distance between any two atoms is less than the sum of the van der Waals radii of the atoms, less the allowed overlap.

The default display for the Bump command is statically connected to the first molecule specified. That is, it is not updated in response to movement of the molecule(s) involved. The Bump command can also set up a monitor that changes dynamically as the molecule(s) are moved. The van der Waals radii used in calculating the overlaps are determined from the elements.dat file and is read in when Insight II is started. The percentage of overlap considered to be unacceptable is a parameter of this command.

Neighbor

The Neighbor command displays the distance between one or more source atoms and their neighbors. Two atoms are neighbors if they are in the same molecule and are separated by three or more bonds.

You can specify whether you want neighboring atoms to be connected by a solid line with the distance displayed between them, or with a dashed line. You can add, delete specific, or delete all of the given type of neighbor displays.

Other options allow you to limit the display of neighbors to only those falling within a specified minimum and maximum distance, or those having a certain element type.

HBond

The HBond command is used to add, and delete some or all of the hydrogen bonds within or between molecules from the display.

A hydrogen bond is considered to be formed when the distance between the proton on the donor atom and the heavy atom acceptor is less than a specified distance, and the angle between the proton acceptor, the proton, and the proton donor is greater than 120 degrees. If hydrogens are not included in the current display, hydrogen bonds are displayed between the heavy atoms oxygen and nitrogen. The distances and angle used for determining whether an acceptor and donor are within hydrogen bonding distance are taken from the file, hbond_file.dat, which is located in the $INSIGHT_DATA library.

The display of the hydrogen bonds differs slightly between intramolecular bonds (within a molecule), and intermolecular bonds (between molecules). Intermolecular hydrogen bonds are displayed with dashed green lines connecting the atoms, along with the associated distances. This display looks and acts exactly like a distance monitor. Intramolecular hydrogen bonds are lighter in color and have no distance displayed. Note that although hydrogen bonds are similar to distance monitors, they can only be deleted with the HBond command.

Energy

The Energy command allows you to examine or to monitor the total energy of a single molecule. You can specify which atomic energies will be used to compute the total energy. You can choose one of the sets of predefined groupings of energy terms, including all atomic energies, only the diagonal terms excluding the hydrogen bonding and cross terms, and only the nonbond terms. You can also specify any group of energies desired. You can also add, remove and/or clear energy monitors.

The source of the parameters used for the energy calculation is the currently assigned forcefield file.

Transform Pulldown

The Transform pulldown contains commands that control the three-dimensional spatial transformations of objects (i.e., rotations and translations). Also included are commands that define certain characteristics of the three-dimensional viewing window.

All objects that are defined in the system may be moved, rotated, scaled, etc., in relation to the frame of reference of the viewing window (screen). Such three-dimensional transformations may be performed in a continuous manner by using the mouse, or the dial slider boxes in the lower left part of the screen. Some of the commands in this group allow these same transformations to be performed in discrete, user-defined steps. In the case of rotation and translation, the transformations can be performed in an object space axis system. Object space axes differ from the screen axes in that they are unique to each object. Object space axes move and rotate with an object when the object is transformed in screen space. The default object space axes are defined by the principal moments of inertia of the object. Alternative definitions can be set up. The object to which the dials are connected is identified immediately under the screen dial boxes.

Commands in this pulldown also allow you to select the object(s) to which the transformations are applied, to set the scale of the objects, and to set the window clipping parameters. Also included are commands to define torsions about bonds, perform superimpositions of molecules, rock any object about the y axis, and define which object the mouse or dials are connected to.

Connect

The Connect command is used to connect the mouse and dials to an object. The mouse and dials control the scale, translation, and rotation of objects. These operations can be performed by using the mouse, the dial slider boxes on the screen, or physical dials.

You can also specify that the given command be performed on world, rather than an individual object or assembly.

By default, whenever more than one object exists, the dials are connected to world, which is a pseudo-association to which all objects in the system belong. Therefore, all objects initially move and scale as one. The Connect command allows you to connect to a particular object or assembly so that it may be moved or scaled independently.

The dials remain connected to the specified object until another Connect command is issued or until a command is given that connects the dials to an object by default. The dials may be reconnected to world at any time by using the Connect command with the World option and no object name.

In the case of rotation and translation, the transformation may be performed in an object space axis system.

Position

The Position command in the Transform pulldown allows you to list or delete alternate positions that have been previously stored with objects.

Reset

The Reset command in the Transform pulldown allows you to apply alternate positions that have been previously stored with objects. These alternate positions are created with the Store command in the Transform pulldown. The positions LAST, CURRENT, and ORIGINAL are automatically generated and are updated whenever you use the commands Connect, Move, Rotate, Scale, Center, Superimpose, and Overlay from the Transform pulldown, or when you use the function keys (<F10> or <F11>) to connect to objects.

Store

The Store command in the Transform pulldown allows you to store alternate positions for objects. These alternate positions can be applied later using the Reset command in the Transform pulldown.

You may name a position with any alphanumeric string of characters and the dollar sign and underscore. However, the names CURRENT and ORIGINAL are reserved and cannot be used.

Axes

The Axes command is used to define the alternate space axes for an object. The alternate space axes define the center of rotation for the object and system in which the object is translated and rotated when the dials are connected in the Alternate space of transform mode. Alternate space axes are convenient for performing such tasks as rotating about the axes running through a helix, or normal to plane. They are also used for positioning and aligning the object via the Move and Rotate commands and are used for positioning sliceplanes when visualizing grids.

The alternate space axes can be defined by using the Moment_of_Inertia of the object, specifying three Atoms or Coordinates, or providing an alternate space transformation Matrix. The Recenter boolean controls whether the alternate space axes are recentered on a new point or whether only their direction is altered.

Center

The Center command in the Transform pulldown is used to define the center of rotation of an object or assembly. The new center can be defined in several ways. For example, you can define the center of rotation as the center of mass of the object or set of objects (default), as a single atom or the coordinates of an atom, as the three-dimensional midpoint of three atoms, or as an arbitrary point in the world system. You can also specify that the given command be performed on world, rather than an individual object or assembly.

If one or more objects of an assembly are translated, the center of rotation is not automatically updated. This update must be done using the Center command.

The center of rotation of world may be redefined by using the World parameter with no object name or mode option.

In the menu version of the Center command, the Position Center parameter may be entered by picking an atom with the mouse. The resulting values are the x, y, z world space coordinates of the atom. Note that this is the same as using the Atom mode, and thus is not the intended use of the position mode.

Move

The Move command translates an object or assembly to a new position on the screen. This can be in the world axis system or the object axis system. The same effect can be obtained by using the mouse, dial boxes on the menu, or physical dials for the translation. However, the Move command provides a means of moving an object by a specific amount, or to a specific location.

Rotate

The Rotate command rotates an object or assembly by a specified number of degrees about the world axis or object axis system.

You can specify the number of degrees in each direction (X, Y, Z), that the object should be rotated. Values must be specified for each direction, even if they are 0. The rotations are always done in the order X, Y, Z.

Scale

The Scale command is used to set or change the scale of one or more objects to a user-specified value. This is useful for resetting objects that have been independently scaled, to a common scale, or for changing the scale by a known amount. The scale of objects specified with the Connect command can be changed in a continuous manner through the use of the mouse or the dials.

Apply

The Apply command is used to apply the current rotation transform to the coordinates of the molecule. This command functions identically to the sequence of operations: Put Molecule Transform ON, Delete Molecule, and Get Molecule with the transformed coordinates.

Clip

The Clip command is used to manipulate the thickness (the distance between the front and back clipping planes) of the viewing window, and the Z position (the midpoint of the window in the z direction) of the viewing window. The viewing window is also referred to as the slab. The thickness can be controlled using the <F12> function key labeled slab thick, and the slab position by the on-screen dial box labeled Slab Pos.

The closer an object is to the front of the viewing window, the brighter it appears. Conversely, the closer an object is to the rear of the window, the dimmer it appears. The percentage of the viewing window spanned by the object determines the range of the depth cueing that is applied to an object. An object spanning the entire window will range from no depth cueing (very bright) to all depth cueing (black). Moving the Z position of the clipping plane is equivalent to translating an object along the screen Z axis. The current position of the center of the viewing window, and the width of the viewing window are displayed in the lower left corner of the screen.

Rock

The Rock command is used to initiate a rocking motion of one or more objects on the screen about the Y axis. This rocking motion is useful for giving a pseudo three-dimensional illusion to the structures. The rocking can be controlled in both speed and magnitude.

Each time the timer fires, the object(s) are rotated by a specified number of degrees. Specifying a larger number of degrees causes a faster rotation rate. By specifying a large value for the magnitude of the rocking motion a rolling motion can be achieved.

Once the Rock command is activated, rocking continues even if other commands are issued, until the Rock command is turned off.

When specifying the object or objects which are to be rocked, you may use a wildcard, but may not specify an assembly object. If rocking is already in progress, the specified objects are added to the rocking motion.

Torsion

The Torsion command is used to define, tabulate, reverse, delete, clear, and set the display style of dihedral angles for up to four bonds in a molecule.

Once you have defined a torsion it becomes the active torsion; an angle monitor as well as a cone indicating the directionality of the torsion are displayed identifying the active torsion. There is only one active torsion at any one time. To deactivate a torsion, click on empty space. To activate a torsion, click on the bond. To reverse the directionality of the torsion, click on the cone; the vertex of the cone is the anchor point of the molecule, while the large part of the cone points toward the moving portion of the molecule.

You can navigate through the defined torsions using either the <F7> key (Next Torsion) or the dial to activate the torsion of interest.

You can also tabulate the defined torsions, and set the display style to serial number or monitor angle values.

Note that you can define a torsion with two mouse clicks: one to select the torsion bond, and one more click on the Torsion icon (in the icon bar) to define/activate the torsion. If a torsion is active, clicking the Torsion icon deletes that torsion.

Figure 17 . Dial Box for Torsion Navigation

Dials

X Rotate

Torsion1

Y Rotate

Z Rotate

Next Torsion

World Scale

Slab Pos

Conn Obj: DHFR
Slab: 50.00 @ 0.00

Forcefield: cvff

Overlay

The Overlay command allows you to overlay one object onto another. The Insight II program knows where every molecule, graph, user-object, contour, etc. is in space. That is, it knows how each such entity has been moved (translated), rotated, and/or scaled. When one graph is overlaid on another graph, for example, the translation, rotation, and scaling of the two graphs is made the same so both graphs appear overlaid. Normally, this command is used to overlay entities of the same kind on one another: molecules on molecules, graphs on graphs, user objects on user objects. However, you may overlay a molecule onto a graph, or a user object onto a contour and so forth. Note, however, that such heterogeneous object overlays may result in displays that are not easy to predict.

Superimpose

The Superimpose command is used to superimpose two molecules on the screen. Sets of corresponding atoms from each molecule are selected and used to perform a minimum RMS alignment of the two molecules. The first (source) molecule is then moved to visually display its superposition on the second (target) molecule.

A minimum of three atoms from each molecule are required for superimposition.

Parameter options in the Superimpose command allow you to select certain types of atoms, such as heavy atoms, backbone atoms, and alpha carbon atoms, as the source spec and the target spec.

Subset Pulldown

The Subset pulldown contains commands related to subsets. A subset is a collection of atoms from one or more molecules. Frequently, the atoms comprise entire monomers or residues. The subset is defined using commands from the Subset pulldown and can be used in commands anywhere a subportion of a molecule can be used. Subsets can be created by explicitly defining monomers, residues, or atoms, or automatically by having Insight II find monomers and residues within a given proximity of selected regions of a molecule. Subsets can also be used in molecular mechanics simulations using Discover.

Get Subset

The Get Subset command is used to create a new subset by reading a subset definition file (.sub) or a molecular data file (.mdf). If an mdf file is specified, the subset definition is read from the atomset section.

Put Subset

The Put Subset command is used to save a subset in an external file. The subset members are written to a subset definition file (.sub extension). The format of this file is consistent with the atomset portion of the .mdf file. Refer to the file format documentation for more information.

Define Subset

The Define Subset command is used to create subsets that describe static, or dynamic, sets of atoms on the basis of atomic attributes. Multiple attributes can be used sequentially, to define, for example, sets having two properties (attributes within specified ranges) simultaneously.

Zone Subset

The Zone Subset command is used to create a subset. The atoms that will belong to the new subset are specified in terms of a central set of atoms and a radius. All atoms that belong to monomers or residues which fall within the spheres described by the set of central atoms and the radius are made members of the new subset.

Interface Subset

The Interface Subset command is used to create a new subset. The atoms that will belong to the new subset are defined in terms of a central set of atoms, a radius, and an object comparison list. All atoms which are contained in monomers or residues that belong to objects in the comparison list and are within the sphere described by the central atom and the radius are made members of the new subset. This command is useful for finding those residues in a protein around an inhibitor.

Template Subset

The Template Subset command is used to create a new subset whose members are sets of atoms that make up specific patterns within a molecule or assembly of molecules. A specific instance of a pattern is used as a template to locate all occurrences of that pattern within a given search domain.

A template is defined by traversing bonds in a molecule along the shortest path between two atoms. The template may be a branched or linear pattern. If linear, only the atoms along the shortest path between the two atoms are included in the template. If branched, all branch structures encountered along the shortest path are included in the template. Branches may be selectively excluded from the template by specifying one or more blocking atoms.

In addition, a subpattern within the template may be specified. In this case, the template matching still occurs, but only those atoms within the subpattern become members of the subset.

Combine Subset

The Combine Subset command is used to perform logical set operations on subsets. The logical operations include union, difference, and intersect.

Copy Subset

The Copy Subset command is used to create a duplicate of the subset you specify. All members of the subset you specify will also be members of the new subset.

Delete Subset

The Delete Subset command is used to delete a subset. Atoms that comprise the subset are not deleted, only the subset abstraction of them.

Rename Subset

The Rename Subset command is used to assign a new name to the specified subset. The New Subset Name must be unique and follow the same syntax restrictions as the Subset Name parameter.

List Subset

The List Subset command is used to display the monomers or residues and atoms that comprise a subset.

Assembly Pulldown

The Assembly pulldown contains commands that act on assemblies or groups of objects.

An assembly is a collection of objects that can be rotated, moved, and scaled as a single unit. It is composed of one or more other objects, which may themselves be assembly objects. This nesting may take place to any depth, but name specification is limited to five levels of nesting. The primary purpose of an assembly is to allow you to move a cluster of objects about its common center of mass.

For several of these commands, value-aids which specify assemblies already known to the system are presented alongside the relevant parameter blocks.

Associate Assembly

The Associate Assembly command creates an assembly comprised of existing objects. An assembly is a logical grouping of objects that can be manipulated as one unit when connected to the mouse or dials. When an assembly is written out, all of its member objects are written out.

Add Assembly

The Add Assembly command adds an object to an existing assembly.

Remove Assembly

The Remove Assembly command removes an object from an existing assembly.

Cell Assembly

The Cell Assembly command is used to specify the size, angles, and table number of the asymmetric unit, which may then be used in crystal and periodic boundary condition operations. This information is also used by the Cell_display, Macro_Cell, Layered_Cell, Symmetry and Soak Assembly commands. The asymmetric unit is also used in solvent calculations and in solvent generations. The Center_in_Cell boolean specifies that the molecule or assembly should be centered within the cell box.

Cell_display Assembly

The Cell_display command displays an object as it appears in a periodic system defined by a given unit cell. Note that the asymmetric unit needs to be defined prior to using Cell_display.

Display modification commands (e.g., Color, Display, CPK, Ball and Stick) work on these periodic atoms (symmetry/lattice offset generated replicates of the asymmetric unit). Ribboning, moving individual replicates, and topological or chemical modification (e.g., Element type, Charge, Potential Type, Bond order/type changes) do not. This is because the periodic atoms mirror many of their parent atoms' attributes, and cannot be changed. However, the Merge command in the Modify pulldown can be used to convert replicates into independent molecules by merging the replicates into another molecule. Once merged, all modification commands (e.g., Color, Move, Ribbon, etc.) are available for use.

Symmetry Assembly

The Symmetry Assembly command is used to create, delete, and display symmetry-related replicates of a molecule. The position of a replicate is calculated directly from the cell parameters (lengths, angles, and space group operator) of a reference molecule.

Display modification commands (e.g., Color, Display, CPK, Ball and Stick) works on these periodic atoms (symmetry/lattice offset generated replicates of the asymmetric unit). Ribboning, moving individual replicates, topological or chemical modification (e.g., Element type, Charge, Potential Type, Bond order/type changes) will not. This is because the periodic atoms mirror many of their parent atoms' attributes, and cannot be changed. However, the Merge command in the Modify pulldown can be used to convert replicates into independent molecules by merging the replicates into another molecule. Once merged, all modification commands (e.g., Color, Move, Ribbon, etc.) are available for use.

The Delete option in the Symmetry Assembly command allows you to eliminate the entire periodic system, leaving only the asymmetric unit.

Soak Assembly

The Soak Assembly command can be used to solvate a molecule. There are three Methods provided. The molecule can either be surrounded by a Layer of solvent (where you specify the thickness), placed in the center of a solvent Sphere (where you specify the atom to place at the center of the sphere, and the radius of the solvent sphere), or a Periodic Boundary Condition (PBC) box previously defined using the Assembly/Cell command can be filled with solvent to generate a bulk model. Solvation is accomplished by placing the molecule in an equilibrated 3D box of solvent and removing those solvent molecules which overlap with atoms in the molecule being solvated. Because any atom overlap causes the whole solvent molecule to be removed the resulting model can be at a lower than expected density. It is important to fully equilibrate the model using molecular dynamics before carrying out any analysis.

The default is to soak with water using the waterbox.psv file provided in the $INSIGHT_DATA directory. $INSIGHT_DATA also contains files for toluene (tolubox), THF (thfbox), paraxylene (pxylenebox), and octanol (octobox). However, any solvent may be used if the necessary solvent files are provided. Soak requires either a .psv or .car and .mdf files for an equilibrated PBC box of the solvent. These can be generated using Insight II (macros are provided in the $BIOSYM_ROOT/$BIOSYM_CONTEXT/gifts/insight directory to help with this task--contact the Customer Support hotline for further information), or using the Amorphous_Cell module.

Solvation is accomplished by placing the molecule in an equilibrated three-dimensional grid of solvent and removing those solvent molecules which overlap with atoms in the molecule being solvated. The default is to solvate with water. However, any solvent may be used for solvation if the necessary solvent files are provided. The Soak Assembly command allows you to:

1.   Specify the atom to be used to define the center of the solvent sphere.

2.   Specify the method of the solvation. Methods available include: adding a layer of solvent of a specified thickness to the object; placing the object in a specified sphere of solvent, or by solvating in a crystal cell.

List Assembly

The List Assembly command lists information about assembly or replicate objects. The details listed are the center of mass, scale, current translation and rotation, transform and rotation matrices, and the component objects for each specified assembly. This command can also be used to list the symmetry-related replicates for a specified object, which list the cell space group information for each replicate.

User Pulldown

The User pulldown contains commands that manipulate the display of user objects and their labels. User objects are read from specially formatted files that describe arbitrary data, such as arrows, text, and dots. User objects frequently are used to annotate models that are currently displayed.

Get User

The Get User command retrieves, displays, and names stored user objects from special format user files. By using the reference option, you can control whether or not the Get command uses an existing object as a reference coordinate system.

Color User

The Color User command modifies the color of the specified user object, user object label, or user object user label. You may type the color specification or select it from the color palette. Colors can be specified using any of the normal methods.

Transparency User

The Transparency User command is used to adjust the degree of transparency in the solid surfaces of a user object. This is achieved by setting the alpha component of all colors in the surfaces without affecting the r,g,b values (see Use of Color for more information). A Transparency Value of 0.0 means fully transparent and a Transparency Value of 1.0 means fully opaque.

Annotate User

The Annotate command is used to create annotations for molecular models. The annotation may consist of lines, arrows, text, circles, open boxes, and filled boxes. For example, you may use annotations to add explanatory comments to a molecular model.

To create an annotation, select the object type (line, arrow, text, etc.), specify an annotation name, select the characteristics you would like for the object (color, size, etc.), then click on the Coord1 parameter.

When the Coord1 parameter is active, you may click in the 3D window to "draw" the object. For text, click the mouse button to create the object, then, with the mouse button still down, drag the mouse to place the text in the desired location. For the other object types, click where you would like the object to begin and, while holding the mouse button down, drag the mouse to the place where the object is to end.

For example, to draw an arrow, click where you would like the arrow to begin, then drag the mouse to the location where you would like the arrow to end. The arrow is drawn as you drag the mouse to illustrate the appearance the arrow will have when you release the mouse button.

After creating the first object, you may continue to add objects to the annotation. Subsequent objects continue to be added to the annotation until a new annotation name is entered into the Annotation name parameter. The annotation is an assembly which contains the objects which have been added to it.

Note that the names for the annotation objects are automatically generated.

Label User

The Label User command controls the creation and positioning of labels for user objects. You can position the label above, below, or to the left or right of the user object. You can also specify the x, y, and z coordinates so that the command positions the corresponding label to the screen position specified by these coordinates.

Options in the Label User command allow you to specify whether the current Label User command operates on a user object label or on a user object user label. A user object label is simply the name of the user object, whereas a user object user label is any arbitrary text.

Charsize User

The Charsize User command is used to modify the size of a specified user label.

List User

The List User command displays information pertaining to the structure and display of a user object. You can direct the information to either the textport or a file.

Spectrum Pulldown

The Spectrum pulldown contains commands to get, put, create, edit, and manipulate spectrums. Spectrums are used to map data values to colors in a variety of coloring and data analysis commands. They may specify very complex mappings through the use of multiple subranges, each being either a solid color or a color ramp. Spectrums can be translated and scaled, and their orientation and other display attributes adjusted to provide the optimal relationship to the rest of the objects on the screen.

Get Spectrum

The Get Spectrum command is used to restore a spectrum from a file. Spectrum save files have the extension .spect, and are created with the Put Spectrum command.

Put Spectrum

The Put Spectrum command is used to save a spectrum to a file. The resulting filename is the spectrum name with the extension .spect.

Edit Spectrum

The Edit command of the Spectrum pulldown is used to invoke the dialog boxes for spectrum creation and editing. Using these dialog boxes you can create new spectrums with specified ranges and colors and then edit these, or preexisting spectrums, in a highly interactive fashion. To get help on specific Spectrum Edit dialog boxes, press the Help button in the dialog box.

List Spectrum

The List Spectrum command displays information about the value ranges and colors of spectrums. Wildcard specifiers are permitted in spectrum names for this command. The detail level may be set to provide from single line output with names and overall ranges to multiple line output with subrange values and colors. You may redirect output from the screen to an output file if desired.

Custom Pulldown

The Custom pulldown contains commands that assist you in executing macro commands. A macro command is defined by you using the Biosym Command Language (BCL). It is, in effect, a command that combines basic commands of the Insight II program.

In order for the Insight II program to know about a macro command, you need to define it. Typically this is done by putting the macro command's definition into the startup file corresponding to the environment variable $WB_LOCAL_INIT (refer to the separate System Guide). Or, you may execute the Source_File command in the Session pulldown (giving as input the name of a file that contains the macro command's definition). Then you may execute the macro command by simply typing its name (and any parameters that it requires). You may list the defined macro commands with the Catalogue command in the Custom pulldown.

In addition, you may add the macro commands to any pulldown (so that they may be executed using parameter blocks rather than just typing the commands) with the Add_To_Pulldown command in the Custom pulldown.

Add_To_Pulldown

The Add_To_Pulldown command allows you to add a new command to any pulldown in the currently active module. The new command corresponds to a pre-defined macro command. These new commands are colored red in the list of commands in the chosen pulldown. In effect, the Add_To_Pulldown command gives you a second means by which you can execute your macro commands. Once a macro command is defined, it can be executed by typing it in. By using the Add_To_Pulldown command, you automatically build a parameter block for the given macro command. Thus, in addition to typing, you can use a menu to execute the macro command.

Catalogue

The Catalogue command allows you to list out all defined macro commands. The list appears in the textport window. It shows each macro command (and its type) along with its parameters (and their types).

Macro_Delete

This command allows you to remove a macro you previously placed into a pulldown by sourcing a valid BCL file. You can replace the macro by again sourcing that BCL file.

Default

The Default command allows you to specify default values for parameters, commands, and pulldowns within each module.

Trigger

The Trigger command allows you to set which (if any) parameter triggers the execution of a command, once that parameter is filled in.

List_Properties

The List_Properties command allows you to list all of the system and user defined properties currently available. The listing can include the Prop Name, its Origin (Sys/User), its Type (Func/Attr), its Class (Mol/Monomer/Atom), its Return_type (Integer/Float/Boolean/String), and if it is a Functional Type, possibly the Macro Name. You can list all of the classes, or using the Property Class parameter, only one. You can also print to the Textport or output the information to a file.

Window Pulldown

The Window pulldown contains commands that act on windows created by the Insight II program. All of the windows created by the program are normal top-level windows which can be manipulated with the window manager. They can be raised, lowered, closed, or iconified just like any other window. The commands in this pulldown are intended to enhance, but not modify or replace the existing window manager functionality. For example, it is possible to close (delete) any single window by selecting the close option from the Window pulldown in the upper left corner of the window's title bar. While also providing this functionality, the Close Window command provides the additional capability of closing several windows simultaneously through the use of wildcards when specifying the window name.

Furthermore, the Window pulldown contains commands which allow you to create and manipulate window layouts. A window layout is used to organize a set of windows so that they may be resized, moved, and iconified as a single unit.

Raise Window

The Raise Window command pops to the front all windows whose names match the input string. The input string may contain wildcard characters to allow raising more than a single window.

Lower Window

The Lower Window command pushes to the back all of the windows whose names match the input string. This provides a quick way of pushing a set of windows at one time.

Close Window

The Close Window command closes all windows whose names match the input string. A wildcarded string may be used to close more than a single window. Note that closing a window deletes the window, as well as any objects which do not appear in any other window. Since the main window of the Insight II program is the primary focus of user interaction for the program, it may not be closed with this command.

Layout_Template Window

The Layout_Template Window command allows creation and manipulation of layout templates. A layout template is a description of the relative positions and sizes of windows within a layout. While the Insight II program provides a couple of simple default templates, it is difficult to anticipate individual preferences for window layouts. Therefore, this command provides the ability for you to define new templates using the current positions of the windows in the layout you have created. In addition, layout templates can be written to and read from files with this command, so that you may reuse the layouts you create in future sessions.

Layout Window

The Layout Window command allows you to create and define window layouts. A window layout organizes a set of windows so that they can be moved, resized, and iconified as a single unit. The layout consists of two components. The first is the layout template which contains of a set of entries, where each entry specifies the relative size and location of a window as a percentage of the total size of the layout. The second component of the layout is the list of windows which are managed by the layout. When the layout is applied, each window is positioned and sized according to the next unused template entry. That is, the first window in the list is placed in the position described by the first template entry, the second window with the second template entry, and so on until there are either no more windows or no more template entries.

One window may be designated as a control window. This window's position and size are used to determine the size and position of all the other windows so that the layout template specifications are satisfied. To move, resize, or iconify all of the windows together, simply perform the operation on the control window. Any window in the layout may be designated as the control window, or you can use no control window, in which case all windows move and resize independently.

Raise_Layout Window

The Raise_Layout Window command pops to the front all windows which are currently managed by the specified window layout.

Lower_Layout Window

The Lower_Layout Window command pushes to the back all of the windows that are currently managed by the specified layout.

Close_Layout Window

The Close_Layout Window command closes a window layout. Closing a window layout deletes the layout as well as all windows which are managed by the layout.

Help Pulldown

There are two types of help for Insight II. Insight_Help invokes the Help Viewer which enables browsing and printing of online help. Pilot_Tutorials allow for interactive Insight II training sessions using the Pilot program.

Insight_Help

The Help Viewer may be used to browse and to print online help.

The Help Viewer consists of a text viewing area, a row of buttons and pulldown menus for traversing through online help, and the Options and Help pulldown menus.

When the Help Viewer is started within Insight II, it is in follow mode. In this mode, the Help Viewer dynamically changes to mirror the current state of Insight II. This feature may be turned off by choosing the Follow toggle switch on the Options pulldown menu.

The Go Forward and Go Backward menu items under the Options pulldown allow you to revisit the last 10 help topics that you have viewed. The Go Forward and Go Backward features may alternatively be selected by the keyboard mnemonics Ctrl-f and Ctrl-b respectively. This eliminates the need to open the Options menu with the mouse.

The Print... menu item under the Options pulldown invokes a window with print options for the currently displayed help. This window is explained below.

The Quit Help menu item under the Options pulldown removes the current Help Viewer. This action has no effect on Insight II. The keyboard mnemonic Ctrl-q may also be typed to quit from help. This is the equivalent of opening the Options pulldown menu and selecting the Quit Help menu item.

The Help pulldown menu contains a single menu item, Help On Help, which displays this help text.

Traversing Help
Online help may be traversed, whether or not the Help Viewer is in "follow" mode, through the use of the buttons and pulldowns directly above the text area. The item farthest to the right, excluding the "Examples" button, is a pulldown menu containing all topics directly below the current topic in the Insight II hierarchy. As you descend a level, the level pulldown for the previous level is replaced with a button, and a pulldown for the new level is displayed to its right. To return to a higher level, choose the button of the level you wish to return to.

Print Window
The print window provides various printing options.

The Print Command is constructed from the highlighted entries from the Printers list and the Print Commands list. If you do not find the desired printer or command, you may edit the Print Command field by hand. The Printers and Print Commands lists are read from the printer_info file created when Insight II is installed. If you are missing printers or commands, talk to your system administrator about adding them.

The Print Selection list allows you to choose at which level to begin printing. The current level is always the bottom one, and is the default selection.

If the Include Sub-Headings toggle button is set, all help below the chosen selection is printed. If this toggle is off, only the selected item is printed. The depth printing can get large very quickly, so use it carefully.

The ASCII/PostScript toggle determines which type of output to direct to the printer.

Pilot_Tutorials

The Pilot tutorial sub-system displays its own help. To invoke Pilot from within Insight II, select the Pilot_Tutorials command from the Help pulldown menu. To view help for Pilot, select the "?" icon from the bottom row of the main Pilot window.

Contour Pulldown (accessed from the Contour icon)

The Contour pulldown contains commands that allow you to create and manipulate the display of contour objects and their labels. Contour objects display values throughout a set of grid data, such as are output by the DelPhi, DMol, or x-ray crystal refinement programs. Contours can be drawn as dots, lines, or solid surfaces, and represent equivalent values of a given quality of a grid.

Contours created from psv files using a revision of the Insight II program earlier than 2.1.0 have no solid data and thus cannot be displayed as solids. Similarly, contours created with the Get Contour command have no solid data and cannot be displayed as solids.

Contours should be saved and restored using the commands in the Session pulldown.

Get Contour

The Get Contour command retrieves contour maps from contour files created prior to the 2.3.0 version of the Insight II program. By using the Reference option, you can control whether or not the Get Contour command uses an object as a reference coordinate system when it retrieves the contours. The Get Command can retrieve a specific contour value, or all contour values from the contour file.

The Get Contour command defines contours as user objects, rather than as contour objects, and thus they may not be manipulated by the Contour commands. User objects created with the Get Contour command have no solid data and can only be represented as wireframe.

Create_Single Contour

The Create_Single Contour command is used to create contours from grid files or grid objects. When reading from a grid file, a grid object is not created.

A contour object is created for the level selected using the slider box connected to the Level Specification parameter. Contours are given the name specified as the Contour Name parameter.

Contours can be created as Big_Dots, Dots, Lines, Solid contours, or created but Undisplayed as dictated by the Display Style parameter. In most cases the outside of a solid contour is the lighted side, but if a solid contour appears as a dark shape, then the normals should be inverted using the Recalculate Contour command.

A contour created in the execution of the Create_Single Contour command is initially given the color specified by the Color parameter. The color can be modified by the Color Contour command.

Create_Range Contour

The Create_Range Contour command is used to create contours from grid files or grid objects. When reading from a grid file, a grid object is not created.

The range of levels may be specified based on the value of the Level Specification parameter. One contour object is created for each level. The contours are given the name specified in the Contour Name Root parameter, with a numeric suffix added to give a unique name for each level.

Contours can be created as Big_Dots, Dots, Lines, Solid contours, or created but Undisplayed as dictated by the Display Style parameter. In most cases the outside of a solid contour is the lighted side, but if a solid contour appears as a dark shape, then the normals should be inverted using the Recalculate Contour command.

Contours created by the Create_Range Contour command are given one of six unique color specifications. These colors can be modified by the Color Contour command.

Clip_Display Contour

The Clip_Display Contour command controls the clipping and display of contour objects. Various options of this command allow you to clip contours using planes, boxes, or spheres in fractional space and Cartesian space.

Color Contour

The Color Contour command modifies either the color of the specified contour, or the color of the specified contour's label. You can choose one of the predefined colors, such as blue, green, red, cyan, yellow, magenta, or white. Or, you can specify a blend of these colors or define a color hue.

Transparency Contour

The Transparency Contour command is used to adjust the degree of transparency in the solid display of a contour. This is accomplished by setting the alpha component of all colors in the contour without affecting the red, green, blue values. See the Use of Color section in the Introduction to the Insight II User Guide for more information on color specification, alpha values, and transparency. A Transparency Value of 0.0 means fully transparent, and a Transparency Value of 1.0 means fully opaque.

Recalculate Contour

The Recalculate Contour command is used to change the contour level, the normals of solid contours, or the display style of a contour. A new contour level can be selected using the slider box connected to the Level Specification parameter. Solid contours have a lit and a dark side which can be controlled by the Flip_Normals parameter. The Display_Style of contours may be Big_Dots, Dots, Lines, Solid surfaces, or Undisplayed.

Label Contour

The Label Contour command controls the creation and positioning of labels for contours. The object name of the contour becomes the contents of the label. You can position the label above, below, to the left of, or to right of the object. You can also specify the x, y, and z coordinates for any Label Contour command, which then positions the corresponding label to the screen position specified by these coordinates.

Charsize Contour

The Charsize Contour command modifies the size of the specified contour's label.

List Contour

The List Contour command displays information pertaining to the structure and display of a contour. Information in the listing includes the fractional space limits available for display, and the fractional limits currently displayed. You can direct the information to either the textport or a file.

Spreadsheet Pulldown

When you pick the Spreadsheet icon, a menu with fourcommands appears. Picking the Spreadsheet icon is equivalent to picking the Spreadsheet pulldown from the lower menu bar, in modules where that option is available.

New Command

The New command creates a new empty spreadsheet.

New_Molecule Command

The New_Molecule creates a new spreadsheet for a selected molecule.

Open Command

The Open command gets information from disk in various file formats to create a new spreadsheet. The file types include the Biosym ASCII format for graphs, and a neutral ASCII table format used by other spreadsheets.

Put Command

The Put command writes out the table data to an ASCII file that can be printed, viewed, and/or edited. The data are written to a file with the .tab format. Each table cell value is separated by tabs.

Spreadsheet Command Summary

The Spreadsheet commands available are organized into pulldown menus which are consistent with most other spreadsheet programs: File, Edit, Data, Format, and Plot. In addition, three icons at the bottom of the spreadsheet window provide direct access to the three spreadsheet Plot commands: Graph, XYZ_Graph, and Histogram.

New File
The New command creates a new empty spreadsheet within a new window.

Open File
The Open command gets information from disk in various file types to fill the present spreadsheet. The file types include: the two Biosym ASCII formats .tbl and .tab, and the neutral ASCII formats for Wingz and Excel (which should actually be the same as .tab). The file type and the name of the file are stored for use by any subsequent Save commands.

Save File
The Save command writes the spreadsheet to a file using the last values for file type and filename used by Open or Save_As. Therefore, this command will not work unless preceded by a Save_As or Open command. Various formats are supported including: the two Biosym text formats (.tab and .tbl), and a free format that simply outputs columns of information separated by a user specified delimiter.

Save_As File
The Save_As command writes the selected cells to the specified file. Various formats are supported including the two Biosym text formats (.tab and .tbl).

Duplicate File
The Duplicate command creates a new spreadsheet that is identical to the present one. This is effectively a Copy Object command.

Transpose File
The Transpose command changes the table display so that information that is displayed down a column is re-oriented to be displayed across a row and vice-versa

Print File
The Print command creates hardcopy output of the selected cells by writing this information in ASCII format to disk. No formatting information is used in preparing this output.

Edit

The Edit pulldown contains those commands used to modify the spreadsheet, including changing the values of the stored data and adding formula(e).

Cut Edit
The Cut command removes the values of the selected cells from the spreadsheet placing them within the global clipboard.

Copy Edit
The Copy command duplicates the values of the selected cell region and then places them in the global clipboard.

Paste Edit
The Paste command uses values previously placed within the clipboard to sequentially replace the values of those cells selected. If there are more cells selected then there are values within the clipboard, then the sequence is restarted at the beginning of the clipboard selection.

Clear Edit
The Clear command resets the Value, or Format, of the selected cell region to empty. Using this command in conjunction with the Search command constitutes a filter operation.

Find Edit
The Find command takes the selected cell region and modifies the selection to represent only those cells whose value falls within the specified constraints.

Select Edit
The Select command allows the user to create a selection that is used throughout the spreadsheet. This selection is highlighted to indicate the members of the set. (NOTE: This command is redundant with the mouse driven selection using the "ragged" selection methods, but is very useful for writing macros. This is also a fall back position if the mouse driven selection can not be completed.)

Insert Edit
The Insert command allows the insertion of cells at the position of the selected cells described. The extents of the selected region will control the number of rows or columns added.

Delete Edit
The Delete command allows the deletion of the selected cell region as described. Currently, this region encompasses one or more rows or columns.

Fill Edit
The Fill command allows the user to supply a single value to all cells, or a range of values in linear and non-linear progression. The row or column major application of the range to the selected cells is controlled by the spreadsheet preference.

Data

The Data pulldown contains those commands to manipulate or make inquiries about the data within the spreadsheet.

Formula Data
The Formula command fills a row, column, or single table_cell to represent the evaluation of the expression specified. This allows the user to apply the expression to multiple cells at once instead of requiring multiple copy and paste operations over a set of table_cells. This formula represents the mathematical combination of existing information within the spreadsheet.

Search Data
The Search command processes the selected cells and modifies the selection to represent those rows or columns which contain cells whose value falls within the specified range.

Sort Data
The Sort command shuffles the selected rows/columns into ascending or descending order depending on the key row(s)/column(s) that are supplied.

Summary Data
The Summary command displays simple statistics about the specified rows/columns. These include the minimum and maximum values, the average and standard deviation, and the median value.

Highlight Data
For spreadsheets created with Decipher, the Highlight command displays a link between graphs, tables, and molecules using color, allowing you to visualize what information was used to create the display.

Recompute Data
The Recompute command recalculates the active spreadsheet. This can be made to be automatic so that any change in spreadsheet values can trigger the automatic reevaluation of all formulas.

Format

The Format pulldown contains those commands to modify how the spreadsheet is viewed. It also includes commands describing how the spreadsheet is manipulated (such as row major versus column major).

Color Format
The Color command changes the color of the selected cells. A single color value is specified.

Cell_Border Format
The Cell_Border command changes the border display of the selected cells. There are four borders for a cell (top, bottom, right, and left) that can be displayed or undisplayed independently.

Display Format
The Display command allows the user to either Hide cells, or Show previously hidden cells. The user must specify whether either the rows or the columns are modified.

Style Format
The Style command controls the Value_Type and format of the display of the values in the selected cells. You can control the justification (Left, or Right) of the value as well as the Length and precision of the display. This does not have any effect on the actual data stored within the spreadsheet.

Column_Width Format
The Column_Width command changes the width of the selected columns.

Row_Height Format
The Row_Height command changes the height of the selected rows.

Protection Format
The Protection command controls the protection of the Value or of the Value_Type of the selected cells. This protection can be turned On or Off.

Preference Format
The Preference command specifies whether icon plotting and other operations are treated row or column major.

Graph Plot
The Graph command creates or adds to an existing graph a set of plots using each column (or row if the preference is row major). The set of plots created are oriented in 3D based on the plot number.

Bar Graph
The BarGraph command creates, or adds to an existing graph, a set of plots using each selection column (or row, if preference is row major). The set of plots created are oriented in 3D based on the plot number and are represented as solid bars. With a dynamic table (INTERACTIVE) bar graphs are dynamically updated, as well.

XYZ_Graph Plot
The XYZ_Graph command creates or adds to an existing graph, a row/column vs. row/column graph on the X and Y axes that can optionally contain a Z axis.

Histogram Plot
The Histogram command creates, or adds to an existing histogram, a description of the distribution of the selected cells in a bar chart (histogram). You can specify the intended range of the data and control the number of bars (or bins) over which the data is distributed.


Viewer Tutorials

As of this release, most tutorials are now available online for use with the Pilot interface. To access the online tutorials for the Viewer module, click the mortarboard icon in the Insight II interface.

Then, from the Open Tutorial window, select Insight II tutorials, then the Viewer module and choose from the list of available lessons:

Lesson 1 Basics

Lesson 2 Macros and Source Files

Lesson 3 Annotation

Lesson 4 Symmetry Operations

Lesson 5 Using Subsets

Lesson 6 Windows and Window Layouts

Lesson 7 Biosym's Spreadsheet

Lesson 8 Atom Selection Tutorial

Lesson 9 Use of Background Job Commands

You can access the Open Tutorial window at any time by clicking the Open File button in the lower left corner of the Pilot window.

For a more complete description of Pilot and its use, click the on-screen help button in the Pilot interface or refer to the Insight II User Guide.




Last updated December 17, 1998 at 04:26PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.