3
Preparing for the Installation
Decide Where to Install
You will be installing Insight II software in a release directory that you select. Whether you are installing on a single workstation or on a networked workstation, we suggest you use a directory such as /usr/msi/980. If you have a previous release already installed on your workstation, you can add the new release in a new subdirectory if you have enough disk space (see Chapter 2, System & Product Requirements for disk space requirements). If you do not have enough disk space, we recommend you copy your current release to tape using the tar command, remove it from your disk, then install the new release. See your system administrator for more information about using tar.
Decide What SGI Platforms to Extract from the CD-ROM
Silicon Graphics
MSI provides two sets of executables for SGI workstations. One supports IRIX 6.2+ for R4000, R5000, R8000, and R10000 processors as 32-bit executables, while the other supports IRIX 6.2+ for R8000 and R10000 processors as a mixture of 32- and 64-bit executables. Unless you are sure that you will be using the software on R8000 or R10000 machines exclusively, we recommend that you accept the default installation of both sets of executables.
Following is a table of MSI platforms and supported SGI chip revisions.
IBM
MSI provides two sets of executables for IBM workstations. One supports AIX 4.1.4+ for RS/6000 and RS2 machines, while the other supports AIX 4.1.4+ for RS/6000 only. The default installation selection supports both. If you are unsure whether you will be using the software on an RS2 platform, we recommend that you accept the default installation of both sets of executables.
Decide What to Extract from the CD-ROM
To make the installation process easier, a graphical interface tool has been provided for installing the release that allows you to selectively install several or all products from the media. Please note that you will only be able to run those products for which you are licensed. An installation script is still provided for installing from non-graphics workstations. You may select interactive workstation software, such as Insight II and its family of products or computational programs and background software such as Discover and DMol.
Questions You Are Asked During the Installation
During the installation, you are asked to provide information about various default settings. Please take the time to prepare this information before starting the installation.
1. Protein Data Bank (PDB) files
- Insight II allows you to access your Protein Data Bank files. The installation procedure allows you to specify the location of these files. Enter the full pathname to the top root directory containing your PDB files. Refer to the Insight II 98.0 User Guide for complete information on setting up the PDB for use with MSI products.
2. Stereo
- Insight II supports both hardware and split pair stereo. The installation utility allows you to indicate whether you have Stereographics or compatible hardware. You may answer yes if you have Stereographics, Crystal Eyes (StereoView), or Tektronix stereo hardware. If you select YES, then you may select the type of stereo activation your system supports: Automatic, or Manual. Select Manual if you have a switch or button on an external box on the monitor which puts the system into stereo mode. Select Automatic if you have the StereoView or Crystal Eyes option with a stereo-ready monitor which is switched into and out of stereo mode by the software. Make sure you answer this question correctly as it is particularly important that Insight II not attempt to set stereo automatically on systems with a manual switch or button, since this confuses the stereo controller.
3. Gifts and tutorials
- If you are installing from CD-ROM, you may conserve disk space by choosing not to unload gifts or tutorials. Set these option buttons accordingly. The disk space requirements are reflected in the window. Links may be made to the tutorial and gifts directories after installation. This is described in detail in the Installing the Software chapter for your media.
Database Resources
Following are databases which may be of use with Insight II software. Contact the specified distributor for availability and ordering information.
Crystal Structure Databases
Cambridge Structural Database (CSD) - LIFE SCIENCES
Dr. O Kennard or Dr. F Allen
Cambridge Crystallographic Data Center (CCDC)
12, Union Road
Cambridge
CB2 1EZ
England
Phone +44 223 336408
- CCDC Representative USA:
- Dr. W L Duax
Medical Foundation of Buffalo, Inc.
Research Laboratories
73 High Street
Buffalo
NY 14203-1196
USA
- CCDC Representative Japan:
- Dr. O Kammori
JAICI
Gakkai Center Building
2-4-16 Yayoi
Bunkyo-ku
Tokyo 113
Japan
Inorganic Crystal Structure Database (ICSD) - C&S
Fachinformationszentrum Energie Physik Mathematik
D-7514 Eggenstein-Leopoldshafen 2
Germany
Phone +45 7247 82-4554
- USA Representative:
- Scientific Information Service Inc
7 Woodland Avenue
Larchmont
NY 10538
Phone 800 247-3825
NRCC Metals Crystallographic Data File (CRYSTMET) - C&S
Manager CAN/SND
Canadian Institute for Scientific and Technical Information
National Research Council of Canada
Ottawa
K1A 0S
Canada
Brookhaven Protein Data Bank (PDB) - LIFE SCIENCES
Protein Data Bank
Chemistry Department, Building 555
Brookhaven National Laboratory
Upton
NY 11973
USA
Phone: 1 516 282-3629
Fax: 1 516 282-5751
e-mail: pdb@bnl.bitnet
Internet Access
- By Gopher:
The PDB is accessible using Gopher software which follows a simple protocol to "tunnel" through a TCP/IP Internet. This is the recommended method for obtaining information and files from the PDB. Gopher software can be obtained via anonymous FTP to boombox.micro.umn.edu. The PDB Gopher server allows access, search, and downloading of the same information and coordinates files as does anonymous FTP, but through a windowed or menu environment. For help accessing the PDB via Gopher, send e-mail to oeder@bnl.gov.
- By Anonymous FTP:
The PDB has an anonymous FTP account on the system: pdb.pdb.bnl.gov (Internet address 130.199.144.1). Files may be transferred to and from this system using your real user name as the password.
Databases of Crystallographic Data
National Bureau of Standards Crystal Database - C&S
NBS Crystal Data Center
National Bureau of Standards
Gaithersburg
MD 20899
USA
Powder Diffraction File (PDF) - C&S
International Center for Diffraction Data
Swarthmore
PA 19081
USA
Chemical Information Storage & Retrieval - LIFE SCIENCES
Daylight Chemical Information Systems
18500 Von Karman Avenue #450
Irvine
CA 92715
USA
Phone 714 586-6927
Molecular Design Limited
2132 Farallon Drive
San Leandro
CA 94577
USA
Phone 415 895-1313
Chemical Design (Chapman & Hall Dictionary of Drugs)
Chemical Design Ltd
7 West Way, Unit 12
Oxford
OX2 0JB
England
Phone +44 865 251483
Chemical Abstracts Service
Chemical Abstracts Service
2540 Olentangy River Road
PO Box 3012
Columbus
OH 43210
Phone 614-447-3600
Beilstein Institute
Varrentrappstrasse 40-42
6000 Frankfurt 90
Germany
DARC
Télésystèmes Questel
83-85 bd Vincent-Auriol
75013 Paris
France
Others
Quantum Chemistry Program Exchange (QCPE) - LIFE SCIENCES
Creative Arts Building 181
Indiana University
804 State Highway 46 Bypass
Bloomington
IN 47405
USA
Phone 812 885-4784
BioMagResBank - NMR
Department of Biochemistry
University of Wisconsin
420 Henry Mall
Madison
WI 53706
USA
Protein/Nucleic Acid Sequence Databases - LIFE SCIENCES
GenBank
GenBank
National Center for Biotechnology Information
Building 38A, Room 8N803
8600 Rockville Pike
Bethesda, MD 20894
USA
Phone: (301) 496-2475
NBRF-PIR
PIR Technical Services Coordinator
National Biomedical Research Foundation
3900 Reservoir Road NW
Washington, D.C. 20007
USA
Phone: (202) 687-2121
- European inquires:
- MIPS: Martinsrieder Institut für Proteinsequenzen
Max-Planck-Institut für Biochemie
D-8033 Martinsreid
Germany
Phone: +49-89-8578-2656
- Asian or Australian inquries:
- JIPID: International Protein Information Database in Japan
Science University of Tokyo
2669 Yamazaki
Noda 278
Japan
Phone: +81-471-239777
EMBL - SwissProt
European Molecular Biology Laboratory
BIOcomputing Programme
Meyerhofstrasse 1
D-6900
Heidelberg
Germany
Phone: 49-6221-387-258
Last updated December 17, 1998 at 04:01PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights
reserved.