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.
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.
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:
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
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.
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.
Data Value Editing
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
The Ligand_Design module provides functionality to help you design candidate ligands.
The Search_Compare module provides functionality for calculating molecular volumes, performing boolean volumetric operations, and for performing systematic conformational searches.
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.
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.
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.
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.
The Xsight module contains a comprehensive set of commands for performing all aspects of macromolecular crystallography.
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.
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.
The Turbomole module provides an interface to Turbomole, a local density functional quantum chemistry program.
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.
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.
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 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 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.
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.
The Environment command allows you to customize the environment of your current Insight II session. The features that you can control include the following:
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.
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.
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).
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.
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.
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.
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.
The Buffer command controls the number of commands stored in the current session's history buffer.
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.
> alias create list 1,3,5 > color ca:list greenIn 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 greenThese 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 QuitTo redefine the alias token Exit, when the alias Exit already exists:
> Alias Create \Exit DoneThis command redefines the alias token Exit to have the value Done. If the backslash is not present, then the command:
> Alias Create Exit Donefirst 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 \ExitHere, the parameter value Exit is passed on to the command. If the backslash (\) is omitted, then the command:
> Sample_command Sample_object Exitresults in the value Quit being passed in.
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.
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.
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.
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.
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.
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.
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.
The Object pulldown contains commands for manipulating objects.
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 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.
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.
The Rename Object command is used to give a new name to a specified 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.
The Axes_Display Object command is used to control the display of the local and alternate axes systems for objects of any class.
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.
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.
The LineWidth Object command is used to set the width of the lines which are used to represent an 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.
The Molecule pulldown contains commands to manipulate molecules.
The Get Molecule command brings a molecule into the working session.
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.
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.
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.
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.
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.
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.
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 Color Molecule command is used to render molecules and molecular attributes in color.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The source of the parameters used for the energy calculation is the currently assigned forcefield file.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Conn Obj: DHFR|
Slab: 50.00 @ 0.00
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The Charsize User command is used to modify the size of a specified user label.
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.
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.
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.
The Put Spectrum command is used to save a spectrum to a file. The resulting filename is the spectrum name with the extension .spect.
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.
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.
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.
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.
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).
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.
The Default command allows you to specify default values for parameters, commands, and pulldowns within each module.
The Trigger command allows you to set which (if any) parameter triggers the execution of a command, once that parameter is filled in.
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.
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.
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.
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.
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.
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.
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.
The Raise_Layout Window command pops to the front all windows which are currently managed by the specified window layout.
The Lower_Layout Window command pushes to the back all of the windows that are currently managed by the specified layout.
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.
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.
The Help Viewer may be used to browse and to print online 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.
The print window provides various printing options.
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.
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 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.
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 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.
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.
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.
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.
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.
The Charsize Contour command modifies the size of the specified contour's label.
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.
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.
The New command creates a new empty spreadsheet.
The New_Molecule creates a new spreadsheet for a selected molecule.
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.
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.
The New command creates a new empty spreadsheet within a new window.
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.
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.
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).
The Duplicate command creates a new spreadsheet that is identical to the present one. This is effectively a Copy Object command.
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
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.
The Edit pulldown contains those commands used to modify the spreadsheet, including changing the values of the stored data and adding formula(e).
The Cut command removes the values of the selected cells from the spreadsheet placing them within the global clipboard.
The Copy command duplicates the values of the selected cell region and then places them in the global clipboard.
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.
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.
The Find command takes the selected cell region and modifies the selection to represent only those cells whose value falls within the specified constraints.
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.)
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.
The Delete command allows the deletion of the selected cell region as described. Currently, this region encompasses one or more rows or columns.
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.
The Data pulldown contains those commands to manipulate or make inquiries about the data within the spreadsheet.
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.
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.
The Sort command shuffles the selected rows/columns into ascending or descending order depending on the key row(s)/column(s) that are supplied.
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.
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.
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.
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).
The Color command changes the color of the selected cells. A single color value is specified.
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.
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.
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.
The Column_Width command changes the width of the selected columns.
The Row_Height command changes the height of the selected rows.
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.
The Preference command specifies whether icon plotting and other operations are treated row or column major.
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.
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.
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.
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.
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.