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CHAPTER 2: NMRanalyst Installation

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.

2.1 Supported Computer Platforms

NMRanalyst is supported on Intel compatible PCs running Red Hat Linux (Enterprise 5 & binary compatibles, e.g., CentOS) 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. 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.

2.2 Contents of the NMRanalyst Distribution

NMRanalyst contains a database of over 15.9 million unique chemical structures. It is shipped on one DVD. The DVD contains a self-extracting installation program for Linux or for MS Windows 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
Self extracting installer of the Red Hat Linux Enterprise NMRanalyst software. Its data subdirectory contains NMR FIDs for the prednisone structure elucidation for test and practise purposes. (980 MBytes)
ANALYST_WIN.exe
Self extracting installer of the Microsoft Windows NMRanalyst software. It contains a UNIX shell with UNIX user commands. Its data subdirectory contains NMR FIDs for the prednisone structure elucidation for test and practise purposes. (970 MBytes)
Manual.pdf
The NMRanalyst manual is contained in the JavaHelp online documentation. This PDF version is optimized for printing. It can be displayed and printed by the Adobe Acrobat reader (free download from http://www.adobe.com/products/acrobat/readstep.html). (3 MBytes)
struct00, struct01,... struct25
These 26 struct?? files contain the FindIt structure database. The NMRanalyst installer copies these files into the proper location during the installation. (2.32 GBytes in total)
dihydrotestosterone
Ca. 200 micro-gram AP 600 MHz proton, gHSQC, gHMBC, and gDQF-COSY datasets for practising the dihydrotestosterone structure elucidation using Bruker format data. (28 MBytes)
gibberellic_acid
Varian 500 MHz 1D proton and carbon, multiplicity edited gHSQC, and gHMBC gibberellic acid datasets. CHAPTER 5: "Tutorial III: Combining Analysis Results" describes the carbon skeleton determination from this heteronuclear data. (6 MBytes)
gibberellic_acid_no1D13C
Varian 500 MHz 1D proton, multiplicity edited gHSQC, and gHMBC gibberellic acid datasets. CHAPTER 5: "Tutorial III: Combining Analysis Results" describes the carbon skeleton determination from this heteronuclear data without using a 1D carbon spectrum. (6 MBytes)
oligomer_3D_SPECTRUM
The analysis of this 500 MHz Varian 3D HNCO dataset is described in CHAPTER 7: "Tutorial V: Additional NMRanalyst Features". For larger 3D datasets see the following human ubiquitin datasets. (3 MBytes)
prednisone
Varian INOVA 500 3.6 mg/ml proton (34 s), carbon (4 h 51 m), gHMBC (1 h 37 m), and gHSQC (48 m 2 s) prednisone in DMSO-d6 for practising the structure elucidation. (8 MBytes)
strychnine
Varian 500 MHz 1D proton and carbon, multiplicity edited 13C-gHSQC, 13C-gHMBC, 15N-gHMBC, gradient DQF-COSY, and DQ 1,1-ADEQUATE spectra for the strychnine alkaloid. CHAPTER 6: "Tutorial IV: Advanced Structure Elucidation" describes its structure elucidation. (19 MBytes)
sucrose_INADEQUATE
Varian UNITYplus 500 MHz 1D carbon and 2D INADEQUATE sucrose datasets. The VNMR created spectrum as well as the FIDs are provided for practising the automated analysis of VNMR pre-processed spectra as described in CHAPTER 4: "Tutorial II: Setting Analysis Parameters". (5 MBytes)
ubiquitin_HNCACB
Varian 600 MHz 3D gradient HNCACB of 0.2 mM 15N and 13C enriched human ubiquitin. The data was acquired with two transients per increment resulting in a challenging S/N. (17 MBytes)
ubiquitin_HNCO
Varian 600 MHz 3D gradient HNCO of 0.2 mM 15N and 13C enriched human ubiquitin. These analysis results can be combined with the 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
Directory with program and supporting files for uninstalling the NMRanalyst software.
UserData
Directory with default input parameter files for the supported spectrum types.
VERSION
Current version and possibly patch level of the NMRanalyst software.
bin
Directory containing programs, libraries, shell scripts, FindIt structures, and chemical shift information.
cygwin
Directory in Windows NMRanalyst to emulate the UNIX Shell and the UNIX commands available from this shell.
data
Small dataset (1D carbon and 2D INADEQUATE of prednisone) discussed in the tutorials.
enscript
Program enscript and supporting files for converting text to PostScript.
gs
Ghostscript program and supporting files for printing PostScript files on non-PostScript printers.
help
NMRanalyst Manual in JavaHelp format for online display.
jre
Sun Java Runtime Environment (JRE), Standard Edition, Version 5.0.

2.3 Preparation for the Linux Installation

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. Insert the NMRanalyst installation DVD in a local drive and the shown DVD logo appears on the desktop
. Right-click on this logo and select [Mount]. Should no auto-mount occur, use the root account to create the mount point and mount the DVD:

  # mkdir /media/NMRanalyst
  # /bin/mount /dev/hdc /media/NMRanalyst
mount: block device /dev/hdc is write-protected, mounting read-only

To permanently enable user mounting of this DVD drive, update the /etc/fstab file. Replace owner by users in the mount line and the mounting line should be similar to:

	/dev/cdrom	/mnt/cdrom	udf,iso9660	noauto,users,exec,kudzu,ro	0	0

2.4 Installing NMRanalyst

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, and double-click the CD/DVD file system icon . If installing under Windows Vista, right click the NMRanalyst installer (the file ANALYST_WIN.exe) 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 and click the [OK] button. Now Double-click the NMRanalyst installer.

To install NMRanalyst on Linux, follow the SECTION 2.3: "Preparation for the Linux Installation" preparation steps. Start the installation program by executing:

 # sh MOUNT_POINT/ANALYST_LINUX.bin

where MOUNT_POINT is the DVD mount directory, likely /media/NMRanalyst. Some Linux shells might fail to run this installer, so specify sh in this command line to execute it. After starting the NMRanalyst installer, follow the on-screen instructions. 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 Linux 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 Linux 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.

2.5 De-installing NMRanalyst

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. (Under Windows Vista, the de-installation needs to be run in the XP compatibility mode. Before running the de-installer, right click on the item 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 and click the [OK] button.) On Windows 2000 and XP, 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.

2.6 NMRanalyst Software Support

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:

http://www.ScienceSoft.net



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