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The NMRanalyst evaluation software with test datasets is available for download over the Internet and the commercial versions are shipped on DVD. For supported hardware and operating system configurations, see SECTION 2.1: "Supported Computer Platforms". The installation DVD contents and the function of supplied top-level directories are described in SECTION 2.2: "Contents of the NMRanalyst Distribution".
A wizard-style installation (SECTION 2.4: "Installing NMRanalyst") and deinstallation (SECTION 2.5: "De-installing NMRanalyst") procedure is used for the supported platforms. SECTION 2.6: "NMRanalyst Software Support" provides pointers for harder to resolve installation and usage challenges.
NMRanalyst is supported on Intel compatible PCs running Red Hat Linux (Enterprise 4, 5, & binary compatibles) or Microsoft Windows (2000, XP, & Vista with modified installation). NMRanalyst is fully functional on Windows Vista. But its installer (built by the InstallAnywhere software) needs to be executed on Vista in the XP compatibility mode. (Right click the NMRanalyst installer and choose Properties. Click the Compatibility tab. Select the check box Run this program in compatibility mode for and select Windows XP (Service Pack 2). Also select the check box Run this program as an administrator.) After installation, NMRanalyst runs under Windows Vista without using the compatibility mode.
The disk space requirements for the NMRanalyst installation are described in SECTION 2.2: "Contents of the NMRanalyst Distribution". Analyzing spectra with NMRanalyst requires about 120 MBytes of virtual memory. The memory size required by the NMRplot spectral displays scales with the size of the data to be displayed.
NMRanalyst contains a database of over 14.5 million chemical structures. It is shipped on a DVD. The DVD contains a self-extracting installation program and the structure database. It also contains additional NMR datasets and most of their analyses are described in the tutorials. After the software installation, consider copying the example datasets to the installation directory to allow other users easy access to them. The NMRanalyst distribution consists of the following top-level directories and files:
ANALYST_LINUX.bin
data subdirectory contains NMR FIDs for the prednisone structure elucidation for test and practise purposes. (980 MBytes)
ANALYST_WIN.exe
data subdirectory contains NMR FIDs for the prednisone structure elucidation for test and practise purposes. (970 MBytes)
ANALYST_WIN_DEMO.exe
Manual.pdf
http://www.adobe.com/products/acrobat/readstep.html). (3 MBytes)
struct00, struct01,... struct23
dihydrotestosterone
gibberellic_acid
gibberellic_acid_no1D13C
oligomer_3D_SPECTRUM
prednisone
strychnine
sucrose_INADEQUATE
ubiquitin_HNCACB
ubiquitin_HNCO
ubiquitin_HNCACB results to determine protein backbone assignments using the protein2log script. (9 MBytes)
The installation directory for the supported platforms, ANALYST.LINUX or ANALYST.WIN, contains the following files and directories after installation:
COPYRIGHT
RELEASE_NOTES
UninstallerData
UserData
VERSION
bin
cygwin
data
enscript
enscript and supporting files for converting text to PostScript.
gs
help
jre
The Linux system-wide NMRanalyst installation requires root privileges. An individual user can install the NMRanalyst software for private use without root privileges.
1. For a system-wide installation, obtain super user privileges now by typing:
% su root's Password:
and by supplying the password. Normally, the user command prompt (%) changes to "#" for the root account.
2. Mount the NMRanalyst DVD for installation. If no local DVD drive is available, use a drive accessible over the network, load the DVD at the remote location, copy the files and directories over the network to the target computer using a recursive copy command. The following command mounts the DVD. The MOUNT_POINT on Red Hat Linux Enterprise 4 and newer is media. The cdrom is used for a read-only CD or DVD drive, while a writable drive would likely be called cdrecorder:
% /bin/mount /MOUNT_POINT/cdrom
Mounting of removable media might not be enabled for regular users. In that case, use the root account instead. To permanently enable user mounting, update the /etc/fstab file. Replace owner by users in the mount line and this line should resemble:
/dev/cdrom /mnt/cdrom udf,iso9660 noauto,users,exec,kudzu,ro 0 0
The installation consists of a simple series of installation windows allowing modification of default installation parameters. With default settings, it takes about ten minutes to install NMRanalyst.
To install NMRanalyst on Windows, log in as Administrator or use an account with system privileges. Microsoft Windows does not allow overwriting files which are in use. Stop running user programs, or reboot the PC. Insert the NMRanalyst DVD, double-click the desktop 
icon, double-click the CD/DVD file system icon 
, and double-click the file ANALYST_WIN.exe for a permanent installation or file ANALYST_WIN_DEMO.exe for a time limited evaluation installation.
To install NMRanalyst on Linux, follow the SECTION 2.3: "Preparation for the Linux Installation" preparation steps. Start the installation program by typing:
# /MOUNT_POINT/ANALYST_LINUX.bin
where MOUNT_POINT is the directory in which the DVD was mounted.
After starting the NMRanalyst installer, follow the on-screen instructions. The evaluation version requires a password to enable its installation. Under Linux, a user cannot eject a DVD if its mount directory is currently being accessed. So change to a directory other than the DVD mount directory (e.g., cd /tmp) before trying to eject the DVD.
On Microsoft Windows, the default installation directory for the software is ANALYST.WIN located on the drive containing the operating system. When specifying a different directory, leave "ANALYST.WIN" as the installation directory name, use a backslash ("\") rather than a UNIX slash ("/") to separate directories in the path name, and avoid pathnames containing special characters (such as a plus sign, comma, semicolon, equal sign, or square bracket) which can cause problems for a UNIX shell. Changing to a different device character works fine, as long as the new device exists and has sufficient disk space.
On Linux, the recommended location for a system-wide installation is /usr/local. The recommended location for a single user installation is the user's $HOME directory. Other preferred locations are /opt, /export/home, /usr, and /home. The installation program also creates a logical link from the chosen installation directory to the directory specified in the Choose Link Folder window during the installation.
To start the installed software on Microsoft Windows, from the 
menu, click 
, click 
, and then click the 
item. If a different location is specified in the Choose Shortcut Folder window during the installation, start NMRanalyst from the chosen location. Alternatively, double clicking the analyst.exe file inside the installation directory also starts NMRanalyst. See CHAPTER 3: "Tutorial I: Using NMRanalyst" for a description of the use of the software.
The Windows NMRanalyst includes a UNIX shell started from the [UNIX Shell] button in the NMRanalyst application window. It contains the standard UNIX file utilities including ftp, zcat, tar, zip, unzip, etc. to help copying datasets. See SECTION 4.1: "The UNIX Shell Window" for details.
On Linux, start the installed NMRanalyst from a shell window by typing:
% analyst
If no logical links were created during the installation, start the program directly from the installation directory: ANALYST.LINUX/bin/analyst. Except for a small dataset inside the ANALYST.WIN and ANALYST.LINUX directories, which is used for the tutorials and installation testing, additional datasets are only loaded when explicitly copied.
The de-installation procedure described here permanently removes NMRanalyst from a user's computer. After the de-installation, NMRanalyst can be installed again. An older version of NMRanalyst should first be de-installed before the newer version is installed.
To un-install, exit from NMRanalyst. On Microsoft Windows, from the 
menu, click 
, click 
, and then click the 
item. If no shortcut is created during the installation, start the Control Panel and double-click on the 
icon. The NMRanalyst installation creates the "NMRanalyst for Windows" entry in the Add/Remove list. Select this item, click the [Change/Remove] button, and follow the displayed instructions.
To un-install NMRanalyst on Linux, type from a shell window:
% uninstall_analyst
If no logical links were created during the installation, execute this command directly from the installation directory: ANALYST.Linux/UninstallerData/uninstall_analyst. User created files and files shared with other applications may not get un-installed. After un-installing, the entire ANALYST.ARCH (replacing ARCH by WIN or LINUX) installation directory can be deleted to remove remaining files.
NMRanalyst is an ongoing medium size software project. Despite best efforts on our part, shortcomings might be discovered and we need to know about them to correct them! For up-to-date support information and contact information, please visit:
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ScienceSoft, LLC www.ScienceSoft.net |
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