NMRPipe Installation Overview The following are GENERAL REQUIREMENTS for installing and using NMRPipe: A working knowledge of UNIX, including creation of shell scripts. One of the supported UNIX systems such as Linux (most all PC versions), Mac OS X, or SFU 3.5 for Windows XP Pro. A user account with C-shell (/bin/csh or /bin/tcsh) as the default shell. X11 Graphics server and the xterm terminal window. A three-button mouse or its equivalent. The installation of NMRPipe posted here provides the following features and versions: Standard Options, including nmrPipe, nmrDraw, nmrWish, TALOS, MFR, DYNAMO, ACME. Conversion tools for Bruker, Varian, and other formats. Special Options, including 1D STD tools, 2D PCA/HSQC series tools, selNMR, and ezProc1D. The most recent versions of NMRPipe for Linux: version linux9 (for glibc2.5) and version linux (for glibc2.3). (Built 8/12 /2008) The most recent versions of NMRPipe for Mac OS X Intel/PPC (mac), and SFU 3.5 on Windows XP Pro (winxp). (Built 8/12 /2008) Versions of NMRPipe for SGI Irix (sgi6x) and Sparc Solaris (sol). (Built 6/2/2008) Discontinued Version of NMRPipe: DEC Alpha OSF (alpha). (Built 5/3/2007)

NMRPipe Installation Files

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Introduction

NMRPipe is an extensive software system for processing, analyzing, and exploiting NMR spectroscopic data. Our main web site for the software, with links to documentation, etc., is:

     http://www.nmrscience.com/nmrpipe.html

     http://groups.yahoo.com/subscribe.cgi/nmrpipe

     setenv NMR_CONT CORRECT_ALL

The NMR Science install procedure for NMRPipe automatically provides the following features and hardware versions:

• Hardware and OS: software versions for the following systems:
  
  
  • linux: Linux Intel PC (Built on Fedora 4, using glibc 2.3).
  • linux9: Linux Intel PC (Built on Fedora 6, using glibc 2.5).
  • winxp: Windows XP Pro (requires Microsoft SFU 3.5 and X11 Server).
  • mac: Mac OS X PPC and Intel (Built on OS X 10.5.2).
  • sgi6x: SGI Irix (Built on IRIX 4.2)
  • sol: Sparc Solaris.
  • alpha: DEC Alpha OSF (obsolete, no longer updated).
  
  
  
• NMRPipe: comprehensive NMR conversion and processing, 1D-4D.
• NMRDraw: interactive phasing, display, 1D-4D peak detection.
• NMRWish: TCL/Tk scripting for custom display and analysis.
• ACME: COSY proton-proton coupling measurement.
• TALOS: prediction of protein phi/psi from chemical shifts.
• MFR: NMR Parameter Fragment Homology Search (Molecular Fragment Replacement).
• DYNAMO: molecular structure analysis, including:
  • Simulated Annealing structure calculation.
  • Simulation of dipolar couplings and protein backbone chemical shifts, estimation of alignment tensor parameters from measured couplings.
  • List, manipulate, and display structure parameters such as backbone angles.

This text describes both the GENERAL and SYSTEM-SPECIFIC details for installation of NMRPipe. Please review these details carefully before installing the software -- this will help us to use our resources in the most effective way as we continue to support, develop and distribute NMRPipe.

NMRPipe is a UNIX-based system, and so it will require a familiarity of UNIX to install and use the software. This means that an NMRPipe user must be familiar with the UNIX command-line and environment, and know how to create and edit UNIX shell-scripts using a text editor. This is true for all versions of NMRPipe, including the Mac OS X and Windows XP versions.

Some web browsers, especially those used on Windows and Mac OS X, may change the extensions of downloaded files, or attempt to decompress any downloaded files which have been previously compressed. Therefore, when downloading NMRPipe files, take care to retain the exact original file names, and disable any automatic decompression or adjustment of downloaded files. The size of the downloaded files should exactly match the posted sizes.

If there are any PROBLEMS installing NMRPipe, PLEASE review the install instructions carefully; the most common problems involve one of these issues:

• The user's default shell must be set to the C-Shell (/bin/csh); this is often done with the UNIX "chsh" command.
• The user must have a .cshrc file in their home directory, which includes the appropriate commands for establishing the UNIX environment variables required by NMRPipe. The neccessary initialization commands can be found in the file README_NMRPIPE_USERS which is created during installation. If these initialization commands are not executed properly, or if the initialization settings are changed by settings for other software, error messages like the following will result:
  • nmrPipe: Command not found.
  • cannot find manpage for 'nmrPipe'
  • Error in startup script: can't read "env(TCLPATH)": no such variable
  • Application initialization failed: Can't find a usable init.tcl
• In some cases, especially on SGI systems and many Linux environments, the fonts required by the nmrDraw application are not present or not loaded properly. The NMRPipe installation includes fonts suitable for most systems; in most cases, this kind of problem can be fixed by executing an NMRPipe font.com initialization script from within the user's .cshrc file.
• Certain graphics environments may not be suitable, depending on the window manager (the program that manages the graphical desktop of the computer) and the color settings (such as 8-bit color or 24-bit color). For example, certain versions of the Linux Gnome Desktop graphics environment using 32-bit color might cause nmrDraw to run slowly or not at all. Such problems can be often be fixed by adjusting the color settings (24-bit color is most common) or using a different window manager (such as Linux KDE instead of Gnome).
• A particular installation of NMRPipe might not be compatible with all versions of a given operating system. For example, the current Mac OS X version of NMRPipe will generally require a system with Mac OS X version 10.4 or higher. In these cases, none of the programs in the NMRPipe system will work unless the operating system is upgraded appropriately.

How to Install NMRPipe: a Quick Overview

The specific steps needed to install NMRPipe will differ depending on the hardware and operating system, and also on how a given computer or its network is configured. The installation will require that you are familiar with UNIX and the UNIX command line, and that you already know how to create and edit UNIX shell scripts.

Some of the NMRPipe directories contain demo data and scripts which require read-write access. For this reason, it is often useful to install "personal" copies of NMRPipe rather than install the software via the "root" account.

The specific details for installing NMRPipe on particular operating systems are given in the sections below. In general, the steps for installing NMRPipe will involve:

1. Set up a system with UNIX, an X11 graphics server, a user account with the C-shell as the default shell, and with the "xterm" terminal window available from the UNIX command-line. The system should have a 3-button mouse or its equivalent.
2. Create a directory for the NMRPipe installation, where you have complete permissions to create, read, write, and execute files.
3. Put the NMRPipe install files into the selected install directory; the required files are as follows, although you may be provided with additional files for extra features or updates:
   • install.com
   (the install script)
   • binval.com
   (an auxiliary script which determines system type)
   • NMRPipeX.tZ (all versions of NMRPipe)
   • talos.tZ (files required for TALOS)
   • dyn.tZ (optional files for TALOS, files required for DYNAMO and MFR).
   • s.tZ (files required for PCA/HSQC Screening, 1D STD, 1D Batch)
4. From an "xterm" terminal window, execute the install.com script; in most cases, no arguments will be required; it will be sufficient to make the install scripts executable, then run the install.com script. Note: Use the command install.com +help to generate a list of install command-line options.
5. During the install procedure, one or more initialization script files will be created. These initialization scripts must be executed from within the ".cshrc" file in the user's home directory. They will establish the environment variables and executable path which are needed to run the components of NMRPipe. The details about the initialization scripts and how to use them in ".cshrc" will be listed in the file README_NMRPIPE_USERS which is also created during installation:
   • com/nmrInit.*.com (where "*" is linux9, mac, winxp, etc.)
   • dynamo/com/dynInit.com (if DYNAMO is installed)
   • com/font.com
   (font initialization, only needed for some systems).
6. Once NMRPipe is installed, and the user's ".cshrc" file has been adjusted appropriately, log out and log in again. Activate an "xterm" terminal window; it should then be possible to use the components of NMRPipe from the "xterm" command-line.

   (Activate the X11 Graphics server if needed, create an "xterm" window)
   (Use the UNIX command chsh if needed to set default shell to C-shell)
   cd /Users/frank
   mkdir nmr
   cd nmr
   (Get files install.com binval.com NMRPipeX.tZ talos.tZ dyn.tZ etc.)
   chmod a+x *.com
   ./install.com
   cd /Users/frank
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again, test the software)
   (Adjust the software settings if needed)

NOTE well that in some cases, the install procedure may generate informational warning message or error messages, but still complete correctly. So, after the installation procedure, you should try TESTING THE INSTALLATION as below. After testing, you may want to make OTHER ADJUSTMENTS, also below.

What Users Should Do to Run NMRPipe

The tools and scripts of the NMRPipe system require use of the C-shell (/bin/csh) or the related T C-Shell (/bin/tcsh) as the user's default shell. Other shells, such as the Bourne Shell "sh", or the "bash" shell, will not be suitable. So, in order to use NMRPipe, users may have to reset their default shell accordingly. The UNIX command "chsh" is commonly used to set the default shell; see the UNIX "man chsh" help text for information on how to use this command on your system.

If the automated installation succeeded, users need only execute the initialization scripts that were created, by adding lines such as the following to their ".cshrc" file. These commands should preferably be added at the very end of the .cshrc file that the NMRPipe environment variables do not get reset accidentally by other application initialization commands. The details about these initialization scripts and how to use them in ".cshrc" will be listed in the file README_NMRPIPE_USERS which is also created during installation.

Also, regarding fonts: only use the "font.com" script if the "install.com" procedure or README_NMRPIPE_USERS file indicates that it is needed for your system (mostly just SGI/IRIX systems, and some versions of Linux):

        if (-e /u/frank/nmr/com/nmrInit.linux9.com) then
           source /u/frank/nmr/com/nmrInit.linux9.com
        endif

        if (-e /u/frank/nmr/dynamo/com/dynInit.com) then
           source /u/frank/nmr/dynamo/com/dynInit.com
        endif

        if (-e /u/frank/nmr/com/font.com) then
           source /u/frank/nmr/com/font.com
        endif

Testing the Installation

In order to confirm that you can access the software correctly, try logging out first, then logging in and using these commands:

           which nmrPipe          (Check that programs can be found)
           nmrPipe  -help         (Run program in help mode)
           man nmrPipe            (Check manual pages)
           bruker (varian delta)  (Run the graphical conversion interface)
           nmrDraw                (Run the graphical interface)

When using graphical programs in the NMRPipe system, note that all versions of the software expect use of a three-button mouse or its equivalent.

Other Adjustments

NMRDRAW: after testing, you may wish to edit the script called "nmrDraw". The font size argument called "-scale" can be adjusted to suit user preferences for text in buttons, menus, etc. The font arguments "-type1" (regular font) and "-type2" (large font) will affect the size of text used for axes and labels, and for text editing windows. Possible values for "-scale", "-type1" and "-type2" include "small", "medium", "large", and "extraLarge".

You can also adjust the nmrDraw window size to compensate for space on the screen used by window manager command panels, etc. Add the options "-xAdj" or "-yAdj" followed by a pixel count to reduce the nmrDraw window size by the given number of pixels (for example " -xAdj 20").

Many NMRPipe applications are actually NMRWish TCL/TK scripts. These use a small number of common font definitions, which can be adjusted by setting environment variables. Examples are listed in the com/nmrInit.*.com file, and look like this:

 setenv NMRPIPE_SMALLFONT  "-adobe-helvetica-medium-r-*-*-*-100-*-*-*-*-*-*"
 setenv NMRPIPE_BIGFONT    "-adobe-helvetica-medium-r-*-*-*-180-*-*-*-*-*-*"
 setenv NMRPIPE_STDFONT    "-adobe-helvetica-medium-r-*-*-*-120-*-*-*-*-*-*"
 setenv NMRPIPE_BOLDFONT   "-adobe-helvetica-bold-r-*-*-*-120-*-*-*-*-*-*"
 setenv NMRPIPE_FIXEDFONT  "-*-courier-medium-r-*-*-*-120-*-*-*-*-*-*"
 setenv NMRPIPE_TYPINGFONT "-*-courier-medium-r-*-*-*-100-*-*-*-*-*-*"
 setenv NMRPIPE_AXISFONT   "-*-lucidatypewriter-bold-r-*-*-*-120-*-*-*-*-*-*"

Installation Problems

If there are install problems, besides reviewing the notes here, see also the next section for system-specific installation details.

ENVIRONMENT VARIABLE PROBLEMS

The most common problem when first using the installation concerns the proper setting of environment variables. As described above, the environment variables needed by NMRPipe are established by the script "com/nmrInit.*.com" created during the install procedure. This script sets environment variables and executable path for the C-Shell; it WILL NOT work for "bash" or "sh" shells.

If there are problems running the software, look at the definitions in your version of "com/nmrInit.*.com". Then, use the "printenv" command to see if the actual current environment is set up as required. In many cases, certain environment variables need by NMRPipe may get reset by other commands elsewhere in ".cshrc". To avoid this problem, put the NMRPipe initialization commands at the end of the ".cshrc" file.

NMRDRAW FONT PROBLEMS

The "nmrDraw" program uses certain "lucida" and "open look" fonts which are not available on all systems by default. The NMRPipe install procedure will attempt to test whether or not these fonts are available, and provide them if needed. The script "com/font.com" is used to provide the fonts on systems which do not have them. This file is usually executed from a user's ".cshrc" file.

If the fonts cannot be found, "nmrDraw" will issue error messages like this one:

       "XView warning: Cannot load font ..."

If this happens, check the definitions in file "com/font.com", and adjust them if needed.

NMRDRAW XVIEW NOTIFIER ERRORS

In some cases, "nmrDraw" may display "XView Notifier Error" or similar messages; this will generally not cause a problem in the actual use of the software. However, in many cases, these error messages can be suppressed by editing the "nmrDraw" script to add or remove a font specification "-fn", for example,

      ... " -fn Courier " ...

Use the unix command "which nmrDraw" to find the script on your installation.

NMRDRAW RUNS SLOWLY, OR NOT AT ALL

Certain graphics environments may not be suitable for nmrDraw, depending on the window manager (the program that manages the graphical desktop of the computer) and the color settings (such as 8-bit color or 24-bit color). For example, certain versions of the Linux Gnome Desktop graphics environment using 32-bit color might cause nmrDraw to run slowly or not at all. Such problems can be often be fixed by adjusting the color settings (24-bit color is most common) or using a different window manager (such as Linux KDE instead of Gnome).

ALL OF THE NMRPIPE PROGRAMS FAIL TO RUN

A particular installation of NMRPipe might not be compatible with all versions of a given operating system. For example, the current Mac OS X version of NMRPipe will generally require a system with Mac OS X version 10.4 or higher. In these cases, none of the programs in the NMRPipe system will work unless the operating system is upgraded appropriately.

NMRPipe is a UNIX-based system, and so it will require a familiarity of UNIX to install and use the software. This means that an NMRPipe user must be familiar with the UNIX command-line and environment, and know how to create and edit UNIX shell-scripts using a text editor. This is true for all versions of NMRPipe, including the Mac OS X and Windows XP versions.

NMRPipe for Windows XP Pro (Interix/SFU 3.5)

The installation steps for Microsoft SFU 3.5 will require an Administrator account. The SFU installation, the X11 graphics installation, and the NMRPipe installation itself, should all be performed using the same Administrator account.

As noted above, some web browsers may change the extensions of downloaded files, or attempt to decompress any downloaded files which have been previously compressed. Therefore, when downloading NMRPipe files, take care to retain the exact original file names, and disable any automatic decompression or adjustment of downloaded files.

BACKGROUND: Microsoft currently provides a Windows-based UNIX environment (Interix), called "Services for UNIX" (SFU). At the time of this writing, SFU 3.5 can be downloaded at no charge from the Microsoft web site. This download provides a comprehensive UNIX environment that can be installed under Windows XP Professional Edition:

Information on Windows Services for UNIX Version 3.5:

http://www.microsoft.com/technet/interopmigration/unix/sfu/default.mspx

SFU 3.5 Download:

http://www.microsoft.com/downloads/details.aspx?familyid=896C9688-601B-44F1-81A4-02878FF11778&displaylang=en

There is now a version of NMRPipe for Windows XP which REQUIRES that users FIRST install Microsoft Services for UNIX 3.5, and a suitable X11 graphics server with the needed fonts. The steps involved follow, with more details below:

1. Download and install Microsoft SFU 3.5 from the Microsoft web site.
2. Adjust Windows "executable checking" security feature in "boot.ini" for compatibility with SFU 3.5 (i.e., set "/noexecute=AlwaysOff").
3. Install and run a PC X11 graphics server.
4. From the SFU "C-shell" window, start an "xterm" terminal window. In order to use the "xterm" command, you will might first have to set the DISPLAY environment variable manually; later on, this can be established automatically via ".cshrc". To set the DISPLAY manually, type:

             setenv DISPLAY 127.0.0.1:0
   

5. In the "xterm" terminal window, follow the usual "install.com" procedure for installing NMRPipe. If desired, you can include the special option "+sfu" to customize the SFU UNIX environment and create a default home directory and ".cshrc" automatically:

             ./install.com +dest /dev/fs/C/nmr +sfu /dev/fs/C/frank
   

6. Once NMRPipe is installed, commands and programs should generally be executed from an "xterm" terminal window, although most will work equally well from the SFU "C-shell" window.

WHICH VERSIONS OF WINDOWS ARE SUPPORTED?

This version of NMRPipe can only be used on systems where SFU 3.5 can be installed. According to information from Microsoft, SFU 3.5 requires Windows XP Professional Edition, and can also be used with certain other versions of Windows, such as Windows 2000 Service Pack 4. You can also search the web for specific information and tips on installing SFU 3.5 on various systems.

INSTALLING MICROSOFT SFU 3.5

NOTE WELL: according to Microsoft, there are aspects of the installation and use of SFU 3.5 that can effect system usability and security. So, as stated above, we recommend that only users who are familiar with both UNIX and PC system management try this.

Follow Microsoft instructions and guidelines for downloading and installing SFU 3.5. There are many options during the install. In particular, note the following:

• SFU 3.5 provides many server-based features, such as Network File System (NFS), and Network Information System (NIS, a system for login password management). These servers are not required for use of NMRPipe.
  
  
• Certain SFU UNIX utilities need to be enabled to adjust the ownership and permissions associated with files etc. These do not seem to affect the use of NMRPipe, so enabling this option does not seem to be required.
  
  
• UNIX is case-sensitive, whereas, Windows records the case of a file name, but does not differentiate based on case. For example:

  
                Windows: "Frank.txt" is the same file as "frank.txt"
                UNIX:    "Frank.txt" is not the same file as "frank.txt"
  
  

  The SFU install procedure can enable case-sensitivity. However, this is not required for installation of NMRPipe. Enabling case-sensitivity carries with it some security risks, since it opens the possibility of replacing system files with files of the same name but different case. So, we recommend that you do not enable full case-sensitivity for the NMRPipe install.
  
  
• By default, some utilities included with SFU 3.5, such as the GNU "gcc" compiler, will not work because they conflict with a Microsoft "executable checking" security feature (DEP mode). Some features of NMRPipe are also affected by this problem. As a work-around, the security feature can be turned off completely (although naturally, this increases potential security risks) by editing the Windows "boot.ini" file, which is usually on the "C:" drive of a PC.

  Note that the "boot.ini" file is often "hidden" and "read-only". So, in order to change it, you might first have to temporarily adjust "Folder Options" in the "Control Panel" in order to "View Hidden Files" and "Display Protected System Files".

  Then, in order to turn off the security feature, edit "boot.ini" and change "/noexecute=optin" to "/noexecute=AlwaysOff". Then, reboot the system.

We tested NMRPipe with this set of SFU install options:

        1. User: NMR 
           Organization: NMRSCIENCE 

        2. Accept the license agreement

        3. Custom Installation: (+ means install all, - means do not install)

           + Utilities
           + Interix GNU Components (+ GNU Utilities, + GNU SDK)
           - NFS
           - Password Synchronization
           - Remote Connectivity
           - Authentication for NFS
           + Interix SDK
           - Active State PERL

        4. NO  Enable Set UID
           NO  Change Default Behavior to Case-sensitive

        5. YES Local User Name Mapping
           YES Use password and group files
           Leave specification of any password/group files blank

           Windows Domain Name: (kept default value)

        6. NIS Domain: (blank)
           NIS Server: (blank)

        7. Install location: C:\SFU\  (default)

X11 GRAPHICS SERVER FOR WINDOWS

In order to use the graphical components of NMRPipe, an X11 graphics server must be running, and it must provide the lucida and open look fonts as used by "nmrDraw". There are several commercial X11 graphics servers which run on Windows-based PCs: including those from "www.starnet.com" and "www.hummingbird.com".

For building and testing this version of NMRPipe, we used the Xming X11 graphics server and Xming-fonts package. If you use this, be sure to download and install BOTH the server AND the fonts package, and install ALL of the fonts after installing the server ... it's also a nice idea to MAKE a little DONATION to the author of this useful software:

     http://www.straightrunning.com/XmingNotes/

When installing an X11 graphics server, it will generally be best to use the same Administrator account as for the SFU 3.5 installation and the NMRPipe installation.

NMRPIPE INSTALL ON SFU 3.5

As just noted, be sure to use the same Administrator account for the SFU 3.5 installation and the NMRPipe installation.

When choosing NMRPipe install locations under Windows, remember that under UNIX it can be difficult to use file names which have space characters or "special" symbols such as $ (dollar sign). For this reason, we suggest that all install and data locations and paths have "simple" UNIX-style names with no spaces or special characters.

As an example, let's say that we will install NMRPipe on the Windows "C" drive under the directory "nmr", and establish a directory "frank" as the default "HOME" directory. In SFU UNIX, the windows "C" drive is "/dev/fs/C". Note that once SFU 3.5 is installed, you can also make UNIX-style symbolic links, for example:

        mkdir /dev/fs/C/users
        ln -s /dev/fs/C/users /u

We can use the "+sfu" option of "install.com" to adjust the login environment automatically; it does this by changing login files in the "/etc" directory. It will also automatically create a ".cshrc" file. To turn off these options, use "+sfu none".

        (start the PC X11 graphics server if needed)
        (open a C-shell window)

        chsh /bin/csh              (to ensure "/bin/csh" is the default shell)

        xterm &

        In the xterm window:

        csh   (start a C-shell)

        cd /dev/fs/C

        mkdir frank   (will be the default home directory)
        mkdir nmr     (will be install location for NMRPipe)

        cd nmr

        (Get files install.com binval.com NMRPipeX.tZ talos.tZ dyn.tZ etc.)

        chmod a+rx *.com

        ./install.com +dest /dev/fs/C/nmr +sfu /dev/fs/C/frank

Once the install completes, you can close all "xterm" and "C-shell" windows, resetart the X11 server, then open a new C-shell window. Most NMRPipe scripts and programs will run from either a C-shell window or an xterm, although using "xterm" is recommended. So, if there are problems using a graphical script from a C-shell window, try running the command from an "xterm" window instead.

CREATING AN XTERM SHORTCUT

The NMRPipe installation includes an example Windows "xterm" shortcut in the nmrbin.winxp/winxp directory ... you can try copying this shortcut to the Windows desktop as a quicker way to start an "xterm" ... note however that an X11 server must be running first for an xterm window to appear. Right-click on the shortcut to adjust its settings as needed for your system. An example of typical shortcut settings:

   Target:   C:\SFU\usr\X11R6\bin\xterm.exe -ls -sb -bg cyan -fg black -fn lucidasanstypewriter-bold-24

   Start in: C:\frank  (set this to your desired home directory)

   Run:      Minimized

   Icon:     C:\nmr\nmrtxt\x11icon.bmp   (in the "nmrtxt" directory of your NMRPipe installation)

Sun Workstations Running Solaris 2

A release of the software specifically for Solaris 2 is available as a "sol" version. If problems occur with the graphical part of the install procedure, you may require Sun's most current installation or patch of the XView graphics library.

Furthermore, the Solaris 2 versions may require definition of dynamic library locations on your system, especially the locations of the XView libraries (usually /usr/openwin/lib). This is done by a command like the following in your .cshrc file:

         setenv LD_LIBRARY_PATH /U5/sun/opt/SUNWspro/lib:/usr/openwin/lib

Sun's Common Desktop Environment

Use the following resource setting to avoid having nmrDraw's pop-up windows closing prematurely:

          Dtwm*focusAutoRaise: False

          $HOME/.dt/sessions/current/dt.resources

Mac OS X

The currently posted Mac software was built on Max OS X, version 10.5.2. The various NMRPipe graphical tools will require that X11 graphics server and libraries have been installed.

Also, some Mac web browsers, especially Safari, may change the extensions of downloaded files, or attempt to decompress any downloaded files which have been previously compressed. Therefore, when downloading NMRPipe files, take care to retain the exact original file names, and disable any automatic decompression or adjustment of downloaded files.

When using graphical programs in the NMRPipe system, also note that all versions of the software expect use of a three-button mouse or its equivalent.

Installation and use of NMRPipe on the Mac requires the following:

• You might need to get the most recent release of X11 for your Mac. There was an update of X11 issued on 9/15/2008 (version XQuartz 2.3.1 xorg-server-1.4.2-apple 17) which can be found at http://xquartz.macosforge.org/trac/wiki. After installing this update to X11, change the settings: X11 > Preferences > Windows > checkmarks beside both "Click-Through Inactive Windows" and "Focus Follows Mouse".
  
  
• Start the X11 graphics server. You can find Mac's X11 server in folder Applications/Utilities. It will be helpful to drag a copy of this application to the Mac OS X command Dock so that you can start and control the X11 graphics server easily at any time.
  
  
• Once X11 is running, use "Applications/Terminal" to create "xterm" terminal windows. Use these windows for all NMRPipe installation and command execution.
  
  
• You have to be using the c-shell (or t c-shell) not bash or some other shell. On the Mac, depending on the specific version of the operating system, there are several places places where a default shell is set. You might want to use all methods which can be found on your system, then restart the machine:
  
  Method I (as of Mac OS X 10.5)
  1. Under System Preferences, open Accounts Preferences.
  2. Unlock preference settings by clicking on the lock icon in the lower left.
  3. Right-click on a User entry and select the Advanced Options menu.
  4. Select /bin/csh (or /bin/tcsh) from the login shell pull-down menu, then click on OK.
  
  
  Method II (Mac OS X 10.4 and Earlier)
  1. Launch the NetInfo Manager application in the folder /Applications/Utilities
  2. Click the lock icon and then authenticate the admin password.
  Click the "users" entry in the property browser window and then click on the desired username.
  3. The property list for the users account will appear in the bottom of the Netinfo Manager window. Click on the "shell" property and change its value to C-shell "/bin/tcsh".
  
  Method III
  • Change your default shell with the unix "chsh" command: chsh -s /bin/tcsh (or just "chsh" for interactive mode).
  
  Method IV
  • The Mac /Applications/Utilities "Terminal" application has a "Preferences" setting for "Execute This Command" which can be set to "/bin/tcsh"

   (Install a 3-button mouse)
   (Use the methods above to set the default shell to C-shell)
   (Update X11 if needed)
   (Drag X11 from Applications/Utilities to the Apple command dock)
   (Execute the X11 application to start the graphics server)
   (Create an "xterm" terminal window)
   (Create a new "xterm" window, which should now be a C-shell)
   cd (go to home directory)
   mkdir nmr
   cd nmr
   (Get files install.com binval.com NMRPipeX.tZ talos.tZ dyn.tZ etc.)
   chmod a+x *.com
   ./install.com
   cd (go back to home directory)
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again, test the software)
   (Adjust the software settings if needed)

Linux Platforms

The PC Linux version of NMRPipe has become especially popular, and it currently has the best processing and analysis benchmarks for any hardware. Before installing NMRPipe on Linux systems, it is often best to first install the most up-to-date Linux operating system components and X11 graphics software and drivers. In particular, systems with 64-bit CPUs should have suitable 32-bit compatibility libraries installed and configured. Note that many 64-bit Linux installs are already configured to allow 32-bit applications, so no special adjustment is needed to install NMRPipe. If problems are noted, check the web for information regarding your particular version of Linux and hardware environment.

When using graphical programs in the NMRPipe system, also note that all versions of the software expect use of a three-button mouse or its equivalent.

Note that the tools and scripts of the NMRPipe system generally require use of the C-shell as the user's default shell. Other shells, such as the Bourne Shell "sh", or the "bash" shell, which is a common Linux default shell, will generally not be suitable. Use your computer's account creation tools, or the UNIX command "chsh" to set the default shell to "/bin/csh" or "/bin/tcsh".

There are two linux versions of NMRPipe, called "linux" and "linux9". The "linux" version of NMRPipe is built under Fedora Core 4, and is suitable for Linux systems that use earlier versions of the Linux glibc library (glibc 2.3). The linux9 version of NMRPipe is built under Fedora Core 6, and uses glibc 2.5. The install.com script will attempt to automatically determine which version is suitable for the given system. The default version is linux9. The version can be specified explicitly using the +type argument:

   ./install.com +type linux

In other respects, installation of NMRPipe on a Linux system can be performed via the "general" steps, for example:

   (Use the command chsh or other method to set the default shell to C-shell)
   (Create an "xterm" terminal window)
   cd (go to home directory)
   mkdir nmr
   cd nmr
   (Get files install.com binval.com NMRPipe.tZ talos.tZ dyn.tZ etc.)
   chmod a+x *.com
   ./install.com
   cd (go to home directory)
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again, test the software)
   (Adjust the software settings if needed)

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last updated: November 5, 2008 / big frank

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