3. Installing the Software Using

The next step is to install the software from the CD-ROM.

If you previously unloaded Insight II software, and later wish to add or remove software, refer to Adding a product on page 26 and Removing a product on page 27.

Installation instructions

These are the steps necessary to install Insight II software products on Silicon Graphics workstations using a CD-ROM drive. We recommend that you read this entire section before attempting to install the products.

Note: All examples shown in this section use /usr as the root directory.

Step 1: Create a release directory:

Note: The installation directory path must be limited to 40 characters or fewer.

To switch between different releases under the same root directory, an alias is provided. After the installation is complete and the newly created cshrc file is sourced, use the following command to switch runtime environment setup:

> set_context <release_number>
Note: This command is only valid when your Insight II software is installed in the above tree structure.

Use the following commands to create the new I2000.1 directory. (If you choose an area other than /usr/accelrys to install the software, substitute that location wherever /usr/accelrys appears in the following instructions. Also note that if /usr/accelrys/I2000.1 or the chosen directory already exists, rename or delete it before proceeding.)

> cd /usr
> mkdir -p accelrys/I2000.1

Step 2: Verify that the CD-ROM drive is mounted correctly

If the CD-ROM drive is not mounted, you will have to mount it before you can begin the installation. To verify that the Accelrys CD is properly mounted, insert the CD in the CD-ROM drive and type the following command to list the CD contents.

For a drive local to the installation machine:

> ls /CDROM

For a drive remote to the installation machine:

> ls /<remote mount point>/CDROM

For example:

> ls /net/iris2/CDROM

This command should return a list of files. If no list of files is returned, please refer to Appendix A., CD-ROM Mounting Instructions for detailed instructions on mounting the CD-ROM.

Step 3: Extract software from the CD-ROM

Local and remote drive

The following instructions apply when you are installing from a local or remote CD-ROM and assume the CD-ROM has been successfully mounted as described in Appendix A.

If you log in remotely to perform the install, you need to set the environment variable DISPLAY so that graphics are displayed on your local device. For example, if you are working on a machine with a hostname of iris102 and remotely logged in to (rlogin) a machine with a hostname of iris163 to perform the install, then after the rlogin you should set the DISPLAY variable to your local machine:

> setenv DISPLAY iris102:0

We recommend that you install as a non-privileged user with write permission to both the /usr/accelrys and the /usr/accelrys/I2000.1 directories, as well as to your Accelrys License Pack directory (usr/accelrys/License_Pack).

Note: The fastest installation times will be obtained by having both the CD-ROM and installation disk (i.e., /usr/accelrys/I2000.1) local to the same machine. This configuration eliminates any possible slowdown due to network traffic.


LICENSING: You will be guided through license installation before extracting the software.

If you have received a license via email, save this information to a file to have ready when you are asked to install it. If you are a maintenence customer and already have a current license installed in your Accelrys License Pack, then the installation will be configured to use that license when you indicate the License Pack location during installation.

Type in the following separate commands:

1.   Change to the installation directory:

> cd /usr/accelrys/

2.   Start the installation script:

> /CDROM/install (local CD-ROM drive)


> /<remote_mount_point>/CDROM/install (Remote
CD-ROM drive)

You are first prompted to verify your DISPLAY environment setting as dscribed above. You are then asked to verify the release context and root directories.

Next you are prompted to install the Accelrys License Pack, or enter the path of a previously installed License Pack.

Note: The path to the License Pack used to configure the installation must match the path used in the License Pack environment setup file called msi_lic_cshrc. You are warned if these do not match, and told how to correct this problem.

Once the License Pack is installed the install tools are transferred to the current directory, if the current directory is writable.

After the tools have been transferred, the Accelrys Installation Utility is started automatically. If you need to start the install process again, run the program from the local directory using the following command:

> ./install

After a few moments, the Accelrys Installation Utility menu appears.

1.   Choose the "Install Software" option by clicking on the button next to the selection.

After you press this selection a dialog box appears allowing you to install a demo or emailed license. Follow the instructions below, or press "Continue".

Using a previously installed license

If you already have an Accelrys license installed in the Accelrys License Pack you are using for this installation, then press Continue. This license is used to determine what products you need to install. Note that the maintenance date must be current in order to enable new software.

Installing an emailed license

If you have already received a license by email and copied it to a file, select the "Install Emailed License" button from the message window.

To install a license, enter the name and path of the license file or files in the appropriate window entry space and press "Install License(s) & Continue." This merges (if necessary) and renames the file to msilicense.dat and copies it to the $MSI_LICENSE_PACK_DIR/licenses directory. The daemon line is automatically modified and the file is filtered to attempt to fix any corruption which may have occurred during transmission or file transfer.

Installing a demo license

If you have received a demo password from Accelrys, select the "Enter Demo Password" button.

If you do not yet have a license or a password, press "Continue" and complete the installation. You may install the license after the installation has been completed although the products for which you are licensed will not be pre-selected during the installation process. See the separate Accelrys License Guide after software extraction.

Whether or not you were able to install a license, the Software Extraction Setup window appears next.

2.   The Software Extraction Setup window contains the following items which you must make sure are set correctly. Refer to the online help for detailed descriptions of each item.

a.   Installation Site Information:

Source: Media Type, Device Name

Destination: Installation Directory (current directory)

b.   Software Selection:

Platform/OS Version Options

Product Group: Insight Workstation Modules or Background/Computational Only

Include Options: Products, Gifts & Tutorials

c.   Product Selection: Select products you desire to unload. If you desire to select only those products for which you are licensed and the products were not pre-selected according to an installed license, refer to your packing list or the table below.

Table 1. License features by product
Product Name
Install Menu Pick
License Feature

















CNX (separate CD)



CNX (separate CD)-



CNX (separate CD)





















Felix (separate CD)



Felix (separate CD)



Felix (separate CD)



Felix (separate CD)



Felix (separate CD)



Felix (separate CD)










































































Note: To reduce diskspace requirements you may select only the products option, and create links to the gifts and tutorial directories on the Release 2000 CD as follows:
> cd /usr/accelrys/I2000.1
> ln -s /CDROM/gifts gifts
> ln -s /CDROM/tutorial tutorial

3.   Select the Commit button once you have verified all settings.

4.   Continue the installation process with the next step.

Note: If you previously installed software and later wish to extract additional software, use the install utility once again, and choose the "Add Products" option from the installation utility menu.

Step 4: Configure the software

At this point, the Configuration Setup window appears on your screen.

1.   Make sure the following paths are set correctly (include the network path if you are accessing software over the net).

a.   Root Location

b.   Insight PDB (if applicable)

2.   Select Default Context. This option appears only if your root directory contains previously installed Accelrys product(s). Refer to the online help for more detail.

3.   Indicate if Stereo is available and desired. If yes, select the method by which Stereo is activated (Automatic or Manual). Note that this option only appears if you are installing Insight.

4.   Select the Commit button once you have completed checking all settings. This will begin the extraction.

5.   If you are installing tutorials and gifts you are prompted to insert the Accelrys Gifts & Tutorials CD after the extraction from the main CD is complete.

Successful Extraction:

When the extraction is successfully completed, the Configuration monitor window appears and configuration automatically begins. At this point, you may remove the CD from the CD-ROM drive and store it for future use, should you wish to install additional products or reinstall the software.

Possible errors during Extraction:

If unexpected output is detected in the EXTRACT_LOG file, a message window appears explaining that the extraction may not have been successful and gives you the option to view the information in the log file. View this information and determine if it is problematic. If the flagged lines from the log file will not cause a problem with the installation (for example, "permission denied" messages when overwriting an installation or adding a different platform), continue the installation process when prompted to do so. A message window appears when the configuration is complete. Examine log files for detailed information concerning the results of configuration.

Installation test procedure

Upon completion of software extraction and configuration, perform the following installation test procedures:

Step 1: Source the cshrc File

To test the products you must have the correct operating environment set up. Perform the following steps to make sure that your environment will be correct each time you log in:

1.   Place the following line in the .cshrc file in your login directory:

> source /usr/accelrys/cshrc

2.   Log out and back in before running the subsequent tests. Your environment will automatically be set to run the Insight II products since the .cshrc file is sourced during the login process.

If you have a floating license, log on to the license server, so that you can bring up the licensing daemons to activate your licensing as described in the next step.

Step 2: Bringing up the License Manager and Vendor Daemons

If you have a floating or token license, you need to bring up the licensing daemons.

Note: Because of potential security problems, it is not recommended to start license daemons as root. We suggest you log on to the license server and run lmup as a non-privileged user.

Enter the following command at the prompt:

> lmup

You should see output similar to the following:

Checking /usr/accelrys/License_Pack/licenses/msilicense.dat
Starting Accleyrs License Daemon
[1] 26194 26195
Log file being placed in /usr/msi/License_Pack/logs/msilicense_1715.log
8/05 12:05:06 (accelrys) Server started on iris138 for: License_Holder
8/05 12:05:06 (accelrys) Insight     DMol     
8/05 12:05:06 (accelrys) MSI_TokenR

You are given online instructions on how to enable the daemon startup at bootup time. If you are able to bring up the license daemon successfully, we recommend that you enable the daemon start-up procedure at this time.

Step 3: Verify the software license

Before running Insight II's products, verify that the license file is in the right place and contains valid licenses. Having already sourced /usr/accelrys/cshrc, the $LM_LICENSE_FILE environment variable should be automatically defined. This variable indicates the location of the license file. Run the license verification program as follows:

> license_verifier

This program reports the validity of your license file on a line-by-line basis. Refer to the Accelrys License Guide for more information on the results of this program.

You may also run this program using the Accelrys Installation Utility from the Diagnostics menu or the view pulldown menu. This will allow for easy scrolling through the information.

Step 4: Verify the installation

Make sure you have examined both extraction and configuration error log files. These can be viewed using the Accelrys Installation Utility from the View pulldown menu or the Diagnostics Menu. Scan for errors and unsuccessful completion of the process. If both error log files look fine and the license file is correct, then you are ready to run the software.

If you have installed Insight II you can test it by typing the command insightII at the prompt. If you are using other Accelrys software use the appropriate command at this time.

> insightII

Step 5: Test products

To verify that the products you have installed are running properly, you should run a few tests. Tutorials are included in the User Guide of each Accelrys product, and these can be used for this purpose. Refer to the User Guide index for each product to find the exact location and topic. Discover sample and timing tests have also been provided for this purpose.

Configure the system and network

Insight II

Top menu bar pulldown order

The order in which the pulldowns are presented in the top menu bar is configurable. The file insight_configure in the Insight II help directory ($BIOSYM/help/insight) defines the order in which the pulldowns appear. The first pulldown name is the left-most pulldown. The names of each pulldown to be configured must appear in the file, entered in lower case, one per line. Pulldowns omitted are ordered by Insight II's own default scheme.

Alpha-Carbon distance matrix

Accelrys does not distribute the full Brookhaven data bank library. Installing a new release of Insight II does not change any such library you may already have on disk. However, if you choose to add or replace files in your Brookhaven library at the same time that you install the release of Insight II, remember that any such changes to the Brookhaven library must be followed by running the pdb_find_distance utility program, if you wish to perform loop searching in Insight II. For details refer to the full description of the pdb_find_distance utility in the Utilities section of the Insight II User Guide.

Default Insight II startup file

Each time you enter Insight II, the program checks to see if you have a UNIX environment variable default called INSIGHT_INIT_GLOBAL defined. By default, this is defined as $INSIGHT_HELP/wbrc. INSIGHT_HELP is an environment variable default defined in the $BIOSYM/data/special/env_defaults file which is set to a pathname, and wbrc is a string which the program uses to determine whether a standard Insight II startup file or a user startup file should be used.The Insight II startup file contains Insight II commands defining key aliases and/or objects useful when starting the program. If INSIGHT_INIT_GLOBAL is defined as $INSIGHT_HELP/wbrc, and if the above startup file exists, then the program executes the commands in the file. If INSIGHT_INIT_GLOBAL is defined as any other filename (you may choose to use one of your own startup files) and if that file exists, then the program executes the commands in that file. If the file to which it refers does not exist, an error is reported. If INSIGHT_INIT_GLOBAL is not defined no action is taken. Note that if you wish to define additional site-dependent commands or variables, be sure to include the above file.

One important class of objects loaded by the Insight II file above is the default color spectrums. These color spectrums are provided for use with advanced coloring operations, such as coloring a molecule by charge. If you do not wish these spectrums to be loaded at startup, simply edit the above Insight II file and comment out the GET SPECTRUM commands by preceding those command lines with a pound sign (#).

It may be convenient to have a variety of Insight II commands executed each and every time you enter the program. For example, you may wish to define aliases, or set the default z plane clipping automatically.

After checking INSIGHT_INIT_GLOBAL, the default INSIGHT_INIT_LOCAL is checked. If defined, and if the file to which it refers is present, that file is taken as a source of Insight II commands which are then executed.

If defined as an environment variable, each of these may be used to refer to more than one file of commands. In this case, each file is executed in order. To define a variable which refers to more than one file, list the files in the definition separated by spaces. For example, the following command defines INSIGHT_INIT_LOCAL for two command files:

> setenv INSIGHT_INIT_LOCAL "my_startup_file /usr/

When starting Insight II with this definition of INSIGHT_INIT_LOCAL, the commands in my_startup_file are executed, followed by the commands in /usr/dept/insight_commands.

The paths used in your variable definitions may contain environment variables themselves. For example:

> setenv INSIGHT_DEPT "/usr/dept"

> setenv INSIGHT_INIT_GLOBAL "$INSIGHT_DEPT/insight_ commands"

In this example, the command insightII executes the commands in /usr/dept/insight_commands when starting up.

A convenient way to use these startup variables is to define
INSIGHT_INIT_GLOBAL for an entire organization or department and
INSIGHT_INIT_LOCAL for personal startup files.

One of the easiest ways to create a file containing your personal startup commands is to copy and edit the insight.log file. Get into Insight II and interactively run all of the commands that you want performed automatically at startup, then exit. The insight.log file now contains those commands. Rename that file to something like yourname.wbrc and edit the file to remove any commands you do not want done automatically. Finally, edit your .login file to define INSIGHT_INIT_LOCAL to your personal startup file. For example, to use a local startup file called local.wbrc, located in the directory /usr/people/joe, use the UNIX command:

> setenv INSIGHT_INIT_LOCAL /usr/people/joe/

Default forcefield file

Insight II supports the CFF91 forcefield, the CVFF forcefield, the ESFF forcefield, and the AMBER forcefield. The environment variables that must be set are:


Points to the directory which contains the rule files, residue libraries, and forcefield files.

Points to the residue library currently being used for potential function atom type assignments. The default is cvffa.rlb.

Points to the potential template rule file being used for potential function atom type assignment when a match cannot be found in the residue library. The default is cvff_templates.dat. If this environment variable is not defined, Insight II uses the hard-coded rules consistent with the CVFF forcefield.

Points to the forcefield file being used for element type look-up and bond-increment look-up. This file must be consistent with the currently assigned residue library and template rule files.

To assign potential function atom types for the CFF91, ESFF, AMBER, or PCFF forcefields, use the Forcefield/Select command to switch to the appropriate forcefield and then execute the Forcefield/Potentials command.

Stereo display


Hardware stereo systems from SGI or Stereographics are supported under Insight II, but you must be somewhat careful to configure the system properly.

The current software uses the STEREO_DEVICE environment variable to set the default value of the Stereo Type parameter to hardware. It also looks for STEREO_TRIGGER when there is no button or switch to switch the monitor into stereo mode. If there is no button or switch, the STEREO_TRIGGER environment variable should be defined (e.g., setenv STEREO_TRIGGER 1).

If you have a stereo problem, examine these environment variables, which are set in the file /usr/accelrys/I2000.1/config/insight/insight_config. Find the lines that contain setenv STEREO_DEVICE and setenv STEREO_TRIGGER.

Most stereo hardware (e.g., Crystal Eyes) have a software-controlled TRIGGER. This means that the user does not have to push a button or a switch and Insight II can put the system into stereo mode. If you have one of these systems you should:


Note that the actual value of STEREO_TRIGGER is unimportant as long as it is defined.

Other systems (e.g., older add-on systems from Stereographics) require you to push a button or switch to put the system into stereo mode. This means that Insight II cannot put the system into stereo mode without user intervention; you must push the button. With configurations which have a stereo-ready monitor from SGI (most newer monitors) and a user-triggered add-on stereo device, it is particularly important that Insight II not attempt to set stereo automatically, since this confuses the stereo controller. If you have to push a button or a switch to get your stereo going, you should make sure that STEREO_TRIGGER is not defined:


If you have user-triggered stereo hardware you should see a split screen with a lower and an upper display window before you hit the stereo button. If you see two slightly offset full-size images it means that you have STEREO_TRIGGER set when it should not be.

The Hardware option of the Stereo command under the Session pulldown means only that you have some kind of stereo hardware and is not dependent on how it is triggered.

By default the Stereo Type parameter is set to side-by-side. If STEREO_DEVICE is defined in the environment, the default value is set to hardware. If hardware is the desired setting, you can set that with:

> setenv STEREO_DEVICE 1

Stereo is accomplished by halving the vertical resolution and drawing every other scan line for each eye. The screen is essentially split into upper and lower halves which are merged by the stereo controller such that one eye sees the top image and the other sees the bottom image. The graphics and the text are adjusted to compensate, but because you are losing vertical resolution, the jaggedness of the lines is worse in the graphics and the characters are somewhat irregular. The textport is updated by the system software which knows nothing about stereo, so the textport is not really useful in stereo mode. If you must use it, make sure that it is completely in the upper or lower half of the screen, because otherwise it wraps around. Also notice that the text is stretched in the y direction, and may seem transparent because only every other line is displayed.


If you do not have a hardware stereo device, you can display a "side-by-side" stereo image. Activate the stereo functionality of Insight II by selecting the Session/Stereo command. Activate the Software selection, and <Execute>. In this case, you need to cross your eyes slightly to see the stereo effect.

Background jobs

If you plan to run background jobs, refer to the Background Jobs chapter.

Moving the release tree

This section describes the steps needed to move the software to another disk location after successfully installing it. Do not attempt this until the software is fully installed and tested in the current location. Also, do not attempt to do this if you are running directly from CDROM.

1.   Move the install directory tree to the new location using the UNIX command mv if on the same disk:

> mv /usr/accelrys /new_location

If on another disk, use the UNIX command tar:

> cd old_directory
> tar -cf - I2000.1 | (cd new_directory ; tar -xf -)

2.   Run the install script again in the new location. Note that this overwrites some product startup scripts:

> cd /new_location/accelrys/I2000.1
> ./install

When you are prompted to verify the path to be used for configuration, enter the complete path for the License_Pack location. Select the Configure/Reconfigure Software option from the Accelrys Installation Utility Menu to configure the software in the new location. Change the Root and PDB file locations as necessary. A new cshrc file iscreated in /new_root_location/cshrc.

3.   Make sure that users change their .cshrc files to source the cshrc file in the new location:

> source /<new_root_location>/cshrc

If you also move the Accelrys License Pack:

1.   Edit the DAEMON line in any floating license files at your site to reflect the new release tree location. These are located in
/new_location/License_Pack/licenses. To do this automatically after sourcing the cshrc file to set up the new environment, you can use the install_license tool on each floating license in $MSI_LIC_PACK_DIR/licenses. This automatically updates the msi DAEMON line.

> mv $MSI_LIC_PACK_DIR/licenses/msilicense.dat \
> install_license $MSI_LIC_PACK_DIR/licenses/backup/\ msilicense.dat

2.   Reconfigure the License Pack as follows:

> cd /<new_root_location>/accelrys/License_Pack/bin
> ./config_license_pack

Modify the License Pack path as necessary.

3.   Reconfigure all Accelrys software installations with a new License Pack location.

> cd /<new_root_location>/accelrys/I2000.1
> ./install

Enter the new path to License Pack when prompted. Select the "Configure/Reconfigure Software" option and press the Commit button. This makes the necessary path edits to the installation files..

Adding a product

You may install an additional product after you have completed the initial install. Please note that you will only be able to run those products you are licensed for.

If you previously unloaded Insight II I2000 software from the CD-ROM and later wish to unload additional software, use the same installation utility as during the initial install. The following steps locate and execute the Accelrys installation utility.

> cd /usr/accelrys/I2000.1

> ./install

Choose the "Add products" option, and follow the installation instructions in Chapter 4.

Note: If you believe a previous installation did not completely install all necessary files, select Install Software... again and force an overwrite.

When adding a product the platforms are automatically set to those currently installed. It is important that you not change the platform setting selected by the tool. If you wish to add another platform you must remove the currently installed platform directories and use the "Install Software..." option of the installation utility. If you need further assistance installing additional platforms please call or e-mail the Accelrys Scientific Support Center.

Removing a product

You may remove a product from your existing Accelrys installation. Please note that you may remove the product as a non-root user provided you have write permissions to the installation.

Follow these steps:

1.   Go to the home directory of your installation by issuing the command:

> cd /usr/accelrys/I2000.1

2.   If you want to start removing separate product(s) type:

> remove_product
Note: Only the products listed on the remove_product's menu can be removed safely without affecting the rest of the installation.

Respond to the display prompts to remove the appropriate products from your installation.

Installing the DataBank overlay

The DataBank files are large databases that require 2 GB of space to install.

Insert the DataBank CD (part no. SM-I2MOD-005-0503-CD04-001):



This README file.


A list of the file checksums.


The install script.


The overlay file. The install script reads this directly.It is not necessary to untar this file manually.

As with the original installation, log in to the machine with the disk containing the Insight II 2005 release. Log in as either the owner of the files in the $BIOSYM location (this is the preferred method) or as root. Source the cshrc file in the root directory of the Insight II installation as you would normally before running Insight II. This ensures that the $BIOSYM and other environment variables are set.

For example, with the overlay files in your current directory, enter the following commands at the UNIX prompt:

> source /usr/accelrys/cshrc  

(or the actual location on your system)

> ./install_overlay

The file checksums can be verified using the UNIX cksum command.

You can find the checksums in the CHECKSUM file at the root of the CD.

© 2005 Accelrys Software Inc.