Contents
December 1998
1. Introduction
- Purpose and Content
- Overview
- Chapter 2: System and Product Requirements
- Chapter 3: Preparing for the Installation
- Chapter 4: Installing the Software
- Chapter 5: Run Time Environment
- Chapter 6: Background Jobs
- Chapter 7: Installing Felix
- Chapter 8: Printing and Peripherals
- Chapter 9: Exporting Insight II Files to Other Applications
- Chapter 10: Common Questions/Troubleshooting
- Chapter 11: Getting Assistance
- Appendix A: CD-ROM Mounting Instructions
- Additional Appendixes
- Available Documentation
- For Each Product
- For Multiple Products
- System Guide
- Common File Formats
- Other Shared Documentation
2. System and Product Requirements
- System Requirements
- Operating Environment
- Workstation Requirements (to run interactive products)
- Silicon Graphics
- Memory
- Physical Swap Space
- Virtual Swap Space
- Media for Distribution
- Software patches
- Workstation Types/Graphics Boards
- OpenGL Graphics Mode
- Operating Systems
- Additional SGI system requirements
- IBM
- Memory
- Swap Space
- Media for Distribution
- Workstation Requirements
- Operating System Requirements
- Graphics Requirements
- X Windows Configuration
- Common Desktop Environment
- GL Graphics Mode
- OpenGL Graphics Mode
- Hardware Stereo
- Additional Systems Software
- Additional Systems Hardware
- Sun
- Operating Systems
- Swap Space
- Product Requirements
- Summary of Product Disk Requirements
- Disk Space
3. Preparing for the Installation
- Decide Where to Install
- Decide What SGI Platforms to Extract from the CD-ROM
- Silicon Graphics
- IBM
- Decide What to Extract from the CD-ROM
- Questions You Are Asked During the Installation
- Database Resources
- Crystal Structure Databases
- Cambridge Structural Database (CSD) - LIFE SCIENCES
- Inorganic Crystal Structure Database (ICSD) - C&S
- NRCC Metals Crystallographic Data File (CRYSTMET) - C&S
- Brookhaven Protein Data Bank (PDB) - LIFE SCIENCES
- Databases of Crystallographic Data
- National Bureau of Standards Crystal Database - C&S
- Powder Diffraction File (PDF) - C&S
- Chemical Information Storage & Retrieval - LIFE SCIENCES
- Chemical Design (Chapman & Hall Dictionary of Drugs)
- Chemical Abstracts Service
- Beilstein Institute
- DARC
- Others
- Quantum Chemistry Program Exchange (QCPE) - LIFE SCIENCES
- BioMagResBank - NMR
- Protein/Nucleic Acid Sequence Databases - LIFE SCIENCES
- GenBank
- NBRF-PIR
- EMBL - SwissProt
4. Installing the Software Using
CD-ROM
- Installation Instructions
- Step 1: Create a release directory
- Step 2: Verify that the CD-ROM drive is mounted correctly
- Step 3: Extract software from the CD-ROM
- Local and remote drive
- Installation of licenses from the CD
- What to do if no licenses were found
- Installing an emailed license
- Installing a demo license
- Step 4: Configure the Software
- Installation Test Procedure
- Step 1: Source the cshrc File
- Step 2: Bringing up the License Manager and Vendor Daemons
- Step 3: Verify the software license
- Step 4: Verify the Installation
- Step 5: Test Products
- Configure the System and Network
- Insight II
- Alpha-Carbon Distance Matrix
- Default Insight II Startup File
- Default Forcefield File
- Stereo Display
- Hardware (SGI and IBM)
- Software
- Background Jobs
- Multiple Platform Installations
- Moving the Release Tree
- Adding a Product
- Removing a Product
5. Run Time Environment
- Installed Environment
- Install Directory Tree
- Descriptions of Insight II Software Directories
- Aliases and Environment Variables
- Discover
- Homology
- Insight II
- Ludi
- Profiles-3D
- License Manager
- Shared Object/Libary Support
- Running Insight II Software
- Insight II Environment
- How to Run Insight II
- How to Run Insight II in Nongraphics Mode
- Using Insight II with X Windows
- Insight II Customizable Resources
- 4DWm Window Manager Resources
- Mwm Window Manager Resources
- Incompatible Window Manager Resources
- DISPLAY Variable Settings
- Running Programs Standalone
- Discover
- DMol
- Felix
- Running Product Tutorials
6. Background Jobs
- Introduction
- Generic Background Job Invocation Scheme
- Running Discover 2.9X on Remote Hosts
- Background Job File Format
- Running Discover 2.9X in Parallel (SGI and IBM SP only)
7. Installing Felix Software
8. Printing and Peripherals
- RS232 Connections on SGI Workstations
- Cable
- Printing
- Attaching a Printer
- Export_Plot and Export_Image Commands
- Find_printer_info Utility
- Inplot Utility
- Modem Setup
- SGI Files
9. Exporting Insight II Files to Other Applications
- Exporting to a Macintosh
- Transferring Files to the Macintosh from a UNIX Workstation
- Example Using ftp
- Example Using Kermit
- Setting the File Type to PICT
- Using MacLink
- Using ResEdit
- Using the PICT File in Applications
- Exporting Plot Files to IBM-Compatible PC Applications
- Create the Plot File for Export
- Transfer the File to the PC
- Convert the Plot File to the Format Needed by the Word Processor
- Importing a TIFF file into a Word for Windows document
- Trademark Acknowledgments
10. Common Questions/Troubleshooting
- Installation Troubleshooting
- Diagnostics Menu
- Create Diagnostics Info File
- List Installed Products
- View Installation History
- View Environment Variables
- View License Verifier Results
- View Extraction Errors
- View Complete Extraction Log
- View Configuration Errors
- View Complete Configuration Log
- Recreate Installation Links
- Using a Remote CD_ROM
- Problem:
- Solution:
- Common Runtime Problems
- Problem:
- Cause:
- Problem:
- Cause:
- Solution:
- Problem:
- Cause:
- Solution:
- Problem :
- Cause:
- Problem:
- Cause:
- Solution:
- Problem:
- Cause:
- Solution:
- Problem:
- Cause:
- Problem:
- Cause:
- Problem:
- Cause:
- Problem:
- Cause:
- Solution:
- Problem:
- Cause:
- Solution:
- Problem:
- Cause:
- Problem:
- Cause:
- Solution:
- Textport Pushing and Popping
- Changing the Location of PDB Files
- Secondary Window Icons and Hardware Stereo
- License Manager
- Background Jobs: Problems in Remote Execution
- Can You Log On?
- Is the Environment Defined?
- Shell Environments
- Environment Definition Files
- Is the Insight II Environment Defined?
- Does Your .cshrc File Write to Standard Output?
- Are the Insight II Directories Installed and Available?
- Running the Software
- Trouble Using PDB Files from the Brookhaven Data Bank
- Can I use Discover and Insight on atoms that are not listed in the forcefield files?
- When I try to do a loop search (SearchLoop), I get error messages
- How can I put titles on my Insight II screens?
- Making an Icon to Run Insight II
- Saving and Reporting Errors
- Uncompressing Utility Source Code
11. Getting Assistance
- Before You Call, FAX, or Email
- How to Contact Us
- North America
- Europe
- Japan
- Sending Email
- Email Examples
- Example 1 -- Non-Application (licensing)
- Example 2 -- Non-application (Sales)
- Example 3 -- Non-application (Installation)
- Example 4 -- Non-application (hardware)
- Example 5 -- Application
- Example 6 -- Application
- Example 7 -- Application
APPENDIXES
A. CD-ROM Mounting Instructions
- CD-ROM Mounting Instructions
- Step 1: Loading the CD-ROM into the drive
- Step 2: Checking for a /CDROM directory
- Step 3: Checking whether the CD-ROM drive is mounted
- Step 4: Mounting the CD-ROM drive:
- On a Local System
- From a Remote System
B. Setting Up Remote Display Systems
- Licensing issues
- Remote display on a UNIX workstation
- Remote display on a Macintosh or PC
- Mouse button mappings
- Setting up X server products
- Single window mode
- X fonts
- Xdefaults settings
- Motif-compliant window manager
- Starting an X server session
C. X-PLOR
- System requirements
- Operating systems
- SGI multiprocessor version
- Using only one license feature
- Integrating X-PLOR into other environments
- From QUANTA
- MSI_XPLOR environment variables
- Installation test procedure
- Verifying the installation
- Testing products
Last updated December 17, 1998 at 04:01PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights
reserved.