frank From the Bax Group at the National Institutes of Health ...
NMRPipe Spectral Processing and Analysis System
LEGACY Installation Guide


HHS logo NIDDK Logo Contact:
   Frank Delaglio, Ph.D.
   (Now at the NIST in the Instititute for Bioscience and Biotech Research)
   frank.delaglio@nist.gov
   delaglio@nmrscience.com

NOTICE

NMRPipe is now distributed via a new site at the Institute of Bioscience and Biotechnology Research. This NIH website is no longer updated.

The new distribution site is here (www.nmrpipe.com redirects to the new site too):

www.ibbr.umd.edu/nmrpipe

LEGACY VERSION, NO LONGER UPDATED
NMRPipe Installation Guide, Install Files, and Sample Data
November 24 2015

NMRPipe logo

NMRPipe is an extensive software system for processing, analyzing, and exploiting NMR spectroscopic data. This web page contains NMRPipe installation files, as well as demo data with example processing and analysis schemes. The main web site for the software, with links to tutorials and documentation is:

http://spin.niddk.nih.gov/NMRPipe

In addition, there are several web-based applications for manipulating chemical shifts, dipolar couplings, Small-Angle X-Ray Scattering data, and molecular structures. The applications include web-based servers for TALOS+, TALOS-N, and SPARTA+ chemical shift analysis. You can find the various servers here:

http://spin.niddk.nih.gov/bax/nmrserver
The NMRPipe system is officially unsupported by the NIH and without warranties or guarantees of any kind. There is an unofficial mailing list for information on use and features of NMRPipe ... you can join and post your own questions and comments by going to the following web page:

http://groups.yahoo.com/neo/groups/nmrpipe/info

Some previous versions of NMRPipe have an expiration date. To override the expiration date, try the following environment variable setting:

     setenv NMR_CONT CORRECT_ALL

The following are GENERAL REQUIREMENTS for installing and using NMRPipe:

  • A working knowledge of UNIX, including use of a text editor, and creation of shell scripts.
  • One of the required UNIX systems such as Linux (most all PC versions), Mac OS X, or SFU 3.5 for Windows XP Pro.
  • The system used for installation must be 32-bit compatible. This means that 64-bit systems must have 32-bit compatibility libraries installed as needed.
  • 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 scroll-wheel mouse or its equivalent.

The installation of NMRPipe posted here provides the following features and versions:

  • Standard Options, including nmrPipe, nmrDraw, nmrWish, TALOS+, SPARTA+, DC, MFR, DYNAMO, ACME.

  • Conversion tools for Bruker, Varian, and other formats.

  • NMRPipe for Linux: version linux9 (Fedora Core 9, glibc2.8, 32-bit) and version linux (Fedora Core 4, glibc2.3, 32-bit). These Linux versions of NMRPipe require 32-bit compatibility libraries when used on 64-bit systems. The install procedure will automatically choose the NMRPipe Linux version that is suitable, so NMRPipe can be installed on most versions of Linux currently in use.

  • A 64-bit version of NMRPipe: linux212_64 (CentOS 6.5, glibc2.12, 64-bit). This 64-bit version will only be installed if you include the option +type linux212_64 for the install.com installation script. The version of the nmrDraw graphical interface included is still the 32-bit version, and no 64-bit version of nmrDraw will be produced. So when installing 64-bit versions of NMRPipe, 32-bit compatibility libraries will still be required. Information on how to install required libraries for recent CentOS and Ubuntu systems is provided below in the System-Specific Installation Notes for Linux.

  • NMRPipe for Mac OS X Intel/PPC (version mac, built on Mac OS X 10.5.8 gcc 4.0.1 XQuartz 2.6.3).

  • NMRPipe for Windows XP Pro running SFU 3.5 (version winxp).

  • NMRPipe for SGI Irix (version sgi6x, built on Irix 6.5 for mips2).

  • NMRPipe Sparc Solaris (version sol, built on SunOS 5.6).

  • C Source Code for programs which read, write, and interpret the NMRPipe data format (directory format in the installation).

  • C Source Code for Creating NMRPipe Plug-In Functions (directory nmruser in the installation).

NMRPipe Installation Files

When downloading software from this web site, you are agreeing to our Terms of Use, including the terms that there is no right to privacy on this system, and that the the software from this web site is not to be redistributed without permission from the author.

Use care when downloading; depending on settings, certain web browsers may try to unpack a given file, convert it to a different text format, or display it as a web page rather than saving it as a file. If you experience such problems, try different methods for downloading and saving the files, or use a different web browser if possible.

Note well that if the file contents or names are changed in any way during download, the install procedure will not work:

  • When downloading, be sure to retain the exact file name shown here, renaming if needed!

  • When downloading, check that the final file size matches the size shown here exactly!

Windows Internet Explorer: Right-Click, "Save Target As"
Linux Mozilla: Right-Click, "Save Link As" ... if a .com file is displayed as a web page, use "File/Save As".
Mac OS X Safari: Right-Click, "Download Linked File (As)"

File Number File Name RequiredPost Date File Size Contents
   File 1 NMRPipeX.tZ Yes Nov 24, 2015 86,276,925 bytes NMRPipe executables and files for Linux and Mac (Version 8.7 Rev 2015.320.15.26)
   File 2 install.com Yes Nov 24, 2015 46,104 bytes Install script
   File 3 binval.com Yes Nov 24, 2015 3,872 bytes Used by install script
   File 4 plugin.smile.tZ No Sep 1, 2016 53,267,711 bytes SMILE MD NUS Reconstruction
   File 5 talos.tZ No Nov 24, 2015 192,502,073 bytes Files required for TALOS-N, TALOS+, and SPARTA+
   File 6 dyn.tZ No Nov 24, 2015 143,850,933 bytes Optional Ramachandran surfaces for TALOS+ graphics, PDB data and all files for DYNAMO and MFR
   File 7 NMRPipeL.tZ No Nov 24, 2015 64,143,867 bytes NMRPipe legacy executables (SGI, Windows XP Pro, Sparc Solaris)

As an alternative to downloading via a web browser, on linux systems with the command wget available, you can download the install files as follows:

   wget http://spin.niddk.nih.gov/NMRPipe/install/download/install.com
   wget http://spin.niddk.nih.gov/NMRPipe/install/download/binval.com
   wget http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipeX.tZ
   wget http://spin.niddk.nih.gov/bax/software/smile/plugin.smile.tZ
   wget http://spin.niddk.nih.gov/NMRPipe/install/download/talos.tZ
   wget http://spin.niddk.nih.gov/NMRPipe/install/download/dyn.tZ
   wget http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipeL.tZ

On Mac OS X systems, you can download the files with the curl command:

   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/install.com
   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/binval.com
   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipeX.tZ
   curl -O http://spin.niddk.nih.gov/bax/software/smile/plugin.smile.tZ
   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/talos.tZ
   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/dyn.tZ
   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipeL.tZ

NMRPipe on a Virtual Machine

As an alternative to installing a hardware-specific version of NMRPipe from above, we now also provide a complex installation of NMRPipe on a CentOS 6.5 Linux Virtual Machine. The virtual machine can be run on most any recent Windows PC, Mac OS X system, or even on another version of Linux. The virtual installation requires either VMware Player software, or VirtualBox software.

File Number File Name RequiredPost Date File Size Contents
   File 1 NMRPipe_CentOS6.5.ova Yes Oct 6 2015 4,055,105,536 bytes NMRPipe on a CentOS 6.5 Virtual Machine

The NMRPipe virtual installation is pre-configured with the username nmruser and the password nmrpipe (all lower case). The root password is also nmrpipe.

As an alternative to downloading this very large file via a web browser, if you have access to a system with the command wget available (most linux systems), you can download the virtual machine as follows:

   wget http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipe_CentOS6.5.ova

On Mac systems, download the file using the curl command:

   curl -O http://spin.niddk.nih.gov/NMRPipe/install/download/NMRPipe_CentOS6.5.ova

The installation details for the Virtual Machine NMRPipe are included below.

NMRPipe Citation Information

F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995).

Introduction to Installation of NMRPipe

The 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 32-bit (Built on Fedora 4, using glibc 2.3).
    • linux9: Linux Intel PC 32-bit (Built on Fedora 9, using glibc 2.8).
    • linux212_64: Linux Intel PC 64-bit (CentOS 6.5, glibc2.12, 64-bit).
    • winxp: Windows XP Pro (Requires Microsoft SFU 3.5 and X11 Server).
    • mac: Mac OS X PPC and Intel (Built on OS X 10.5.8 gcc 4.0.1 XQuartz 2.6.3).
    • sgi6x: SGI Irix (Built on IRIX 6.5)
    • sol: Sparc Solaris (Legacy Version 7.3 of NMRPipe, built on SunOS 5.6; ).

    * The 64-bit version linux212_64 will only be installed if you include the option +type linux212_64 for the install.com  installation script.

  • 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.
  • TALOS-N: prediction of protein phi/psi and chi from chemical shifts.
  • SPARTA+: prediction of protein chemical shifts from structure.
  • DC: Dipolar Coupling Calculations.
  • 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.

If there are any PROBLEMS installing NMRPipe, PLEASE review the install instructions carefully, including the section about INSTALLATION PROBLEMS below.

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

The most common installation 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, or by system-specific methods described below.

  • 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 necessary 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'
    • NMRTXT: Undefined variable
    • Error in startup script: can't read "env(TCLPATH)": no such variable
    • Application initialization failed: Can't find a usable init.tcl
    • error while loading shared libraries:libxview.so
    • error while loading shared libraries:libtcl8.4.so
    • error while loading shared libraries:libtk8.4.so
    • error while loading shared libraries:libBLT24.so
    • "Can't find a usable init.tcl
    • XView error: Cannot open connection to window server

    As noted elsewhere, it is important to LOG OUT and LOG IN AGAIN after changing the ".cshrc" file in order for the NMRPipe initialization to become active. Since other configuration changes might require restarting the computer, it is best to perform a complete restart if possible.

    If the NMRPipe initialization is performed properly, several NMRPipe-related environment variables will be defined. Use the UNIX command printenv to list the current environment variables, in order to check that the NMRPipe-related ones are defined. for example:
    
        % printenv | fgrep -i nmr 
    
        TCL_LIBRARY=/u/delaglio/nmrtcl/tcl8.4
        BLT_LIBRARY=/u/delaglio/nmrtcl/blt2.4z
        NMRBIN=/u/delaglio/bin/linux9
        NMR_IO_SELECT=0
        NMRPIPE_TCL_LIB=/u/delaglio/nmrtcl/tcl8.4
        NMRPIPE_BLT_LIB=/u/delaglio/nmrtcl/blt2.4z
        NMRCHECK=ALL
        NMRTXT=/u/delaglio/nmrtxt
        NMR_AUTOSWAP=1
        NMRPATHSET=TRUE
        NMR_IO_TIMEOUT=0
        NMRLIB=/u/delaglio/local/linux9/lib
        NMRBINTYPE=linux9
        NMRPIPE_TK_LIB=/u/delaglio/nmrtcl/tk8.4
        TK_LIBRARY=/u/delaglio/nmrtcl/tk8.4
        NMR_TCLTK8=TRUE
        NMRBASE=/u/delaglio
    
    
  • Many NMRPipe applications make use of output from C-shell scripts, many of which may execute a user's .cshrc file when invoked. So, it is important that the commands in .cshrc do not produce any text output when the .cshrc file is executed, or some NMRPipe applications may fail. You can test for this by counting the characters produced when the .cshrc file is executed directly, which should produce the output 0:
       csh ~/.cshrc | wc -c
    
  • Many recent 64-bit versions of Linux do not install the 32-bit libraries required by NMRPipe. In this case, all of the programs of NMRPipe will fail to run. See the notes on Linux Platform installation below for more information.

  • 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. If the required fonts are not available, the nmrDraw program may fail and generate an error message such as:
    XView error: Cannot open connection to window server
    
    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. In other cases, such as Linux Fedora Core 12, the fonts required by nmrDraw are not available by default, but can be downloaded and installed with a command like the following:
         yum install xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-100dpi 
         yum install xorg-x11-fonts-75dpi  xorg-x11-fonts-ISO8859-1-75dpi 
         yum install xorg-x11-fonts-misc
    
  • Certain Linux environments, such as Ubuntu, don't have "Helvetica" and some other common fonts. This can affect the appearance of NMRWish-based graphical applications, such as the varian and bruker commands. Installing the following font package might help:
        apt-get install msttcorefonts 
    
  • 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, or cause problems in other graphical applications like TALOS+. Such problems can be often be fixed by adjusting the color settings (24-bit color is recommended) or using a different window manager (such as Linux KDE instead of Gnome).

  • In order to run the nmrDraw program, Mac OS X users might have to install updated versions of Mac's X11 graphics server. They might also need to adjust X11 mouse focus settings. More details are given in the Mac OS X installation notes below.

How to Install a Hardware specific Version of 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 three-button scroll-wheel 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 usual 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 (optional, files required for TALOS+ and SPARTA+)
    • dyn.tZ (optional, files required for DYNAMO and MFR).

  4. Depending on how the NMRPipe install files are obtained, it will be necessary adjust the file permissions so that it is possible to read all of the install files and to execute the install scripts. This will generally be performed via the UNIX command chmod, for example:
        chmod a+r  *.tZ *.Z *.tar
        chmod a+rx *.com
    
  5. 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.

    If a specific version of NMRPipe is desired use the +type option. For example to use the 64-bit Linux version (linux212_64) instead of the default linux9 version:
       ./install.com +type linux212_64
    
  6. 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).

  7. Once NMRPipe is installed, and the user's ".cshrc" file has been adjusted appropriately, log out and log in again. Note that it is important to LOG OUT and LOG IN AGAIN after changing the ".cshrc" file in order for the NMRPipe initialization to become active.

    After logging in again, activate an "xterm" terminal window; it should then be possible to use the components of NMRPipe from the "xterm" command-line.

In summary, the NMRPipe install procedure will look something like this example, where the home directory is /Users/frank:
   (Use methods as needed to set default shell to C-shell)
   (Activate the X11 Graphics server if needed)
   (Create an "xterm" window which has a C-shell command-line)
   cd /Users/frank
   mkdir nmr
   cd nmr
   (Get files install.com binval.com NMRPipeX.tZ talos.tZ dyn.tZ etc.)
   chmod a+r  *.tZ *.Z *.tar
   chmod a+rx *.com
   ./install.com
   cd /Users/frank
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again)
   (Start an xterm window, 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.

As a convenience, the install.com procedure above can be adjusted to read the installation files from some other source location, for example from a CD-rom. This is done by the install.com +src option. In such a case, only the files "install.com" and "binval.com" need to be in the current directory. For example, if all of the install files are stored together on the CD-rom mounted as /media/cdrom and the home directory is /Users/frank:

   
   (Use methods as needed to set default shell to C-shell)
   (Activate the X11 Graphics server if needed)
   (Create an "xterm" window which has a C-shell command-line)
   cd /Users/frank
   mkdir nmr
   cd nmr
   cp /media/cdrom/install.com .
   cp /media/cdrom/binval.com .
   chmod a+rx *.com
   ./install.com +src /media/cdrom
   cd /Users/frank
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again)
   (Start an xterm window, test the software)
   (Adjust the software settings if needed)

The installation procedure performs several software and graphics tests to check the status of the installation. In some cases, these tests might issue warning messages even though the installation completes properly. In some cases, these tests may fail in a way which interrupts the installation. If this happens, you can suppress the post-installation software tests with the +nopost option, for example:

   ./install.com +src /home/frank/tar +nopost

How to Install the Virtual Version of NMRPipe

  1. Get and Install VMware Player or VirtualBox. On PC hardware, the installation of these applications might require enabling virtualization options in the computer’s BIOS. Consult the application documentation for additional installation details.

    At the time of this writing, VMware Player and VirtualBox applications can be found here:

    http://www.vmware.com/products/player
    https://www.virtualbox.org/wiki/Downloads
    
  2. Use the virtual application (VMWare Player or VirtualBox) to unpack the NMRPipe_CentOS6.5.ova file. The virtual machine is large (~ 5Gb) and will grow larger with use, so choose a suitable location, and keep in mind any automated backup procedures that might be in use on your computer.

  3. Run the NMRPipe Virtual Machine. Running the virtual machine is like turning on a PC – an operating system will start in the usual way, but in its own window.

  4. First Time Configuration. When you start the virtual machine for the first time, you might see a message that “long mode” for 64-bit systems will be disabled … this is expected, and not a problem. On PC hardware, you also might see a message asking that you first enable virtualization options (Intel VT-x) in your computer’s BIOS. And, you might see a message asking whether the Virtual Machine was moved or copied -- select the “Copied” option.

  5. Adjust BIOS Settings of the Computer. If needed, restart the computer, enter the BIOS setup during startup, and adjust the BIOS options to enable virtualization as needed.

  6. Log in to Virtual Linux. When the virtual machine starts, you can log in via the “nmruser” user account. The password for the "nmruser" account is “nmrpipe” and the root password is also "nmrpipe" (all lower case). Note also that the Virtual Machine can be configured so that it is possible to drag and drop files and folders between the Virtual Machine window and the Desktop of the host operating system.

  7. Use NMRPipe. Once you log in as “nmruser”, you can open a terminal window from the command panel at the top of the desk top. All the usual facilities of NMRPipe will be available.

  8. Configure the Virtual Machine environment and Linux. Consult the virtual application (VMWware or VirtualBox) documentation for details on configuring the virtual player for options such as use of removable devices, shared folders, printing, networking and software updates. You can configure the virtual Linux operating system as you would any other Linux installation. The root password for the virtual machine is “nmrpipe”.

  9. Exit the Virtual Machine. When you are done with a session, don’t exit the virtual machine by closing the window via the usual “X” icon – this is the equivalent of unplugging a PC while it is running, and might make the virtual machine unusable. We also recommend that you do not suspend the virtual machine. Instead, when exiting the virtual machine, be sure to shut it down via the system menus for “Shutdown”, just as you would for an actual PC.

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.

As noted above, it is important to LOG OUT and LOG IN AGAIN after changing the ".cshrc" file in order for the NMRPipe initialization to become active.

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 scroll-wheel 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

There are a few common difficulties with installation of NMRPipe, and these generally relate to the various environment variables required to use the software, or to the font settings used by the "nmrDraw" program.

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.

The necessary initialization commands can be found in the file README_NMRPIPE_USERS which is created during installation.

If the various NMRPipe environment variables are not defined properly, "Undefined variable" or "library" error messages will be generated, for example:

  • NMRTXT: Undefined variable
  • Error in startup script: can't read "env(TCLPATH)": no such variable
  • can't find a usable init.tcl
  • error while loading shared libraries:libxview.so
  • error while loading shared libraries:libtcl8.4.so
  • error while loading shared libraries:libtk8.4.so
  • error while loading shared libraries:libBLT24.so
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. As noted elsewhere, it is important to LOG OUT and LOG IN AGAIN after changing the ".cshrc" file in order for the NMRPipe initialization to become active.

Font Problems in NMRDraw and NMRWish Applications

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
    XView error: Cannot open connection to window server

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

Alternatively, on some Linux systems, such as Fedora Core 12, fonts needed by NMRDraw are not available by default, but can be downloaded and installed with the following command:

     yum install xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-100dpi 
     yum install xorg-x11-fonts-75dpi  xorg-x11-fonts-ISO8859-1-75dpi 
     yum install xorg-x11-fonts-misc 

Certain Linux environments, such as Ubuntu, don't have "Helvetica" and some other common fonts. This can affect the appearance of NMRWish-based graphical applications, such as the varian and bruker commands. Installing the following font package might help:

    apt-get install msttcorefonts

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
Graphics Applications Such as TALOS+ Have Distorted Displays

Certain graphics environments may be problematic for nmrDraw and other graphical applications, such as the TALOS+ Ranachandran display. This can sometimes depend on the window manager (the program that manages the graphical desktop of the computer) or 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), by using a different window manager (such as Linux KDE instead of Gnome), or by updating the display drivers. In the most difficult cases, we have sometimes resorted to changing graphics hardware ... in the experience of NMRPipe's author, NVidia graphics hardware (rather than Radeon or Intel) seems to be the best choice for NMRPipe.

Recently, some versions of Linux include special tools for entering Asian language text, such as SCIM. Some of these "Input Method" tools may cause problems with NMRDraw and other graphical programs. If you have problems on Linux systems entering text into graphics programs or using graphical menus, etc, find and disable any special input methods such as SCIM that might be running.

On Mac OS X, NMRDraw Will Not Run, or Freezes

See the Mac OS X installation notes below for details on configuring software and settings for nmrDraw.

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.

In the case of current Linux versions, NMRPipe requires 32-bit compatibility libraries when run on 64-bit hardware. If these libraries are not installed, every NMRPipe program will issue an error messages such as command not found even though the program is available on the executable path and the NMRPipe environment variables are set properly. In these cases, use the appropriate commands to install 32-bit libraries etc. as needed -- the details will depend on your version of Linux, and might be something like one of the following:

    sudo apt-get install ia32-libs
    yum install glibc
    yum install glibc.i686


System-Specific Installation Notes

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.

The sections below provide information and examples for installing NMRPipe on specific systems.


NMRPipe for Windows XP Pro (Interix/SFU 3.5)

This release of NMRPipe for Windows XP Pro makes use of Microsoft Windows "Services for UNIX" (SFU 3.5). It also requires a suitable X11 Graphics Server, such as Xming. According to Microsoft, there are aspects of the installation and use of SFU 3.5 that can effect system usability and security. So, we recommend that only users who are familiar with both UNIX and PC system management try this installing this release.

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.
  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+r  *.tZ *.Z *.tar
        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, restart 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
Note that this library setting is usually established already if the NMRPipe automated installation script was used.

Sun's Common Desktop Environment

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

          Dtwm*focusAutoRaise: False
This value can be set by using the CDE Window Style Manager utility, or it can be set manually by modifying the file:
          $HOME/.dt/sessions/current/dt.resources

Mac OS X

The currently posted Mac software was built on Max OS X version 10.5.8 using gcc 4.0.1 and XQuartz 2.6.3. The various NMRPipe graphical tools will require that an X11 graphics server and libraries have been installed. Also, the graphical tools expect the use of a three-button scroll-wheel mouse or its equivalent.

Generally, NMRPipe facilities are operated from the command-line of an xterm terminal window. In some cases, the nmrDraw program will not work when used from a Mac xterm terminal window. If problems arise using nmrDraw from an a Mac OS X xterm window, try using the Mac OS X terminal application instead. The terminal application can be found in the Mac OS X Applications/Utilities folder.

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.

Recently, some Mac OS X systems may come initially configured to automount the shared directories "/net" and "/home", even if no such network directories are present. This can cause some components of NMRPipe to start very very slowly or freeze, especially nmrDraw, and all the nmrWish-related commands such as "bruker", "varian", and "talos.tcl". This happens because these programs will first search a set of directories for libraries that they require, including the "/net" directory. Usually, this search happens very quickly. In this case however, the programs hang when they try to search the network directories which are not actually connected or available.

You can see whether the "/net" and "/home" directories are automounted by typing the command:

   df -k
If these directories are listed but not actually used or available on your network, you can edit the file "/etc/auto_master" to comment out the appropriate entries, then re-boot the computer. Specifically, insert '#' as the first character of an entry, for example:
   #/net                   -hosts          -nobrowse,nosuid
   #/home                  auto_home       -nobrowse

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

  • An X11 graphics server must be installed, properly configured, and running. Current versions of Mac OS X require that you download and install a recent version of the XQuartz X11 graphics server, which can be found at http://xquartz.macosforge.org/landing/.

    Once an X11 graphics server is running, adjust its settings: on the X11 Preferences Windows tab, set checkmarks ON beside "Click-Through Inactive Windows" "Focus Follows Mouse" and "Focus on New Windows":

    macx11pref

  • Since the X11 graphics server should be started in order to install or use NMRPipe, 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. If problems arise using nmrDraw from an xterm window, try using the Mac OS X terminalapplication instead. If you use the Mac OS X terminal application, be sure to configure the Preferences so that the terminal window uses the C-shell.

  • As noted presviously, NMRPipe requires use of the c-shell (or t C-shell) not bash or bourne 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.
    3. Click the "users" entry in the property browser window and then right-click on the desired username to select Advanced Options.
    4. 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"
As noted in the Overview, the NMRPipe install procedure performs several software and graphics tests to check the status of the installation. If these tests fail in a way that interrupts the installation, you can suppress the post-installation checks using the +nopost install option.

So, the typical steps for installing NMRPipe on a Mac system will be:

   (Install a three-button scroll-wheel mouse)
   (Use the methods above to set the default shell to C-shell)
   (Update X11 from http://xquartz.macosforge.org/landing/)
   (Configure X11 window focus settings)
   (Drag X11 from Applications/Utilities to the Apple command dock)
   (Execute the X11 application to start the graphics server)
   (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+r  *.tZ *.Z *.tar
   chmod a+rx *.com
   ./install.com   (Use +nopost if graphics problems interrupt the install) 
   cd (go back to home directory)
   (Edit .cshrc to insert NMRPipe initialize commands)
   (Log out, log in again, test the software)
   (Try Mac "terminal" app if running nmrDraw from "xterm" fails)
   (Adjust the software settings if needed)

Linux Platforms

There are currently three linux versions of NMRPipe, version linux for legacy linux systems, version linux9, and 64-bit version linux212_64. By default, the linux9 version will be installed. If you wish to try the 64-bit version, you must explicitly choose it when running the install script:

   ./install.com +type linux212_64

Most Linux systems will require additional libraries and fonts in order to use NMRPipe. All versions of NMRPipe have components such as nmrDraw that will require 32-bit libraries. If the correct libraries are not installed, NMRPipe components will generate error messages or possibly not run at all. Furthermore, if the required fonts are not installed, the nmrDraw program might fail with a message like the following:

    XView warning: Cannot load font
    XView error: Cannot open connection to window server

Lately, many Linux systems do not include the C-shell by default; in these cases, you will have to install a C-shell on your system before being able to install or use NMRPipe. On some linux systems, the C-shell can be installed with a command such as:

   yum install csh

When using NMRPipe for the first time, if an error message indicates that a required library is missing, you can try using the library name directly to find a suitable update. For example, for the error message Error while loading shared libraries: libX11.so.6 try:

   yum install libstdc++.so.6

As an example, on Ubuntu 14 64-bit systems, the following commands were required in order to use NMRPipe:

     apt-get install csh

     dpkg --add-architecture i386

     apt-get update
     apt-get install libc6:i386
     apt-get install libstdc++6:i386
     apt-get install libx11-6:i386
     apt-get install libxext6:i386
     apt-get install msttcorefonts
     apt-get install default-jre
     apt-get install default-jdk

On CentOS 6 and 7 64-bit systems, first edit the file /etc/yum.conf and add the following line so that 32-bit versions of libraries will be installed:
     multilib_policy=all

After adjusting the yum configuration file above, install the required libraries:

     yum install libgcc
     yum install glibc
     yum install libX11.so.6
     yum install libXext.so.6
     yum install libstdc++.so.6
     yum install xorg-x11-fonts-75dpi
     yum install xorg-x11-fonts-ISO8859-1-75dpi

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 NMRPipeX.tZ talos.tZ dyn.tZ etc.)
   chmod a+r  *.tZ *.Z *.tar
   chmod a+rx *.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)

NMRPipe Demonstration Data

NMRPipe provides the following facilities, which can be illustrated by trying the various demos in the software installation and demo data archives below.

  • NMRPipe includes special tools to help automate the conversion of time-domain data from Bruker, Varian, and JEOL Delta, with adjustment for digital oversampling. This includes updates to accommodate newer Bruker TopSpin format data. (bruk2pipe var2pipe delta2pipe bruker varian delta).
  • General-purpose data format conversion tools are provided, so that most any sequential data format can be used to generate input for NMRPipe, and processed data can be saved in other forms. (bin2pipe byteAdjust pipe2xyz conv.tcl txt2bin.tcl txt2pipe.tcl pipe2txt.tcl).
  • NMRPipe includes comprehensive facilities to process, rephase and display multidimensional data, including options for Maximum Entropy Reconstruction (MEM), Linear Prediction (LP), and Maximum Likelihood Frequency Maps (ML), and Principal Component Analysis Linear Prediction (PCA-LP). Rigorous inverse processing facilities are also provided for optimal use of these special reconstruction methods. (nmrPipe nmrDraw, cbcaconh.tar.Z sample3d.tar.Z etc).
  • The nmrDraw program can display multidimensional time- frequency- and interferogram data, and multiple 1D overlays. The program also provides real-time interactive phasing of multiple 1D spectra, with automated reconstruction of imaginary data.
  • Recent versions of nmrDraw now also include facilities for correlated cursors and data positioning for viewing two or more related spectra.
  • NMRPipe's pipeline-based processing schemes are intrinsically parallel, and multidimensional processing scripts can be easily modified for distributed processing in multi-CPU environments (nmrShell nmrCsh sample3d.tar.Z).
  • NMRPipe includes flexible, effective methods to replace bad values in multidimensional data using Linear Prediction (badnoe.tar.Z).
  • NMRPipe provides a variety of approaches for reconstruction of Non-Uniform Sampled Data (NUS), using MEM, Maximum Likelihood, and Matrix Decomposition (nusdemo2d.tar.Z and nusdemo3d.tar.Z)
  • Rapid and Effective Automated Peak Detection for 1D-4D (nmrDraw nmrWish).
  • Extensive Line-Shape fitting functions, including direct fitting of pseudo-3D data such as relaxation series or J-modulated series (autoFit.tcl showEvolve.tcl fitXY.tcl relax.tar.Z jmod.tar.Z).
  • Create simulated time or frequency domain data, including qualitative simulations of common spectral types such as "HNCA" etc (autoFit.tcl simSpecND simTimeND sim3d.tar.Z).
  • Create and draw strip plots, projections, and overlays (scroll.tcl stripPlot.tcl proj3D.tcl view2D.tcl). Latest options include strip plots for multiple spectra, with drag and drop options to adjust strip order (valpha.tar).
  • Predict protein backbone angles based on backbone chemical shifts (talos.tcl) (See demo data in "talos/test" directory of installation).
  • Simulate and display protein backbone chemical shifts based on backbone angles (nmrWish DC showCS.tcl, directory mfr/demo).
  • Calculate J-couplings from Karplus parameters (See directory "mfr/demo" in the installation).
  • Simulate or fit and display Dipolar Couplings (See directories "dynamo/demos/dchn" "mfr/demo" in the installation).
  • Estimate protein alignment tensor parameters from measured dipolar couplings without prior knowledge of the structure. (See directory "mfr/demo" in the installation).
  • Visualize tensor parameters with respect to a PDB file. (rotDC.tcl rotPCS.tcl and directory "mfr/demo" in the installation).
  • List or display Protein PDB backbone and sidechain angles, visualize ramachandran trajectory for one or more proteins or fragments (angles.tcl dynAngles.tcl scrollRamaCS.tcl directory mfr/demo, directory dynamo/demos/ubiq).
  • Analyze Protein PDB for H-bonds and secondary structure and turn classification (ss.tcl).
  • Find coordinate or torsion RMSD between two or more structures, form overlay (ov.tcl, directory dynamo/demos/dcnh).
  • Simulated annealing structure calculation, including NOEs, J-coupling, torsion restraints, radius of gyration, pseudo-contact shifts, and dipolar couplings (directory "dynamo/demos").
  • Search the PDB Database for NMR Parameter Homology (directory fr/demo).

Optional Demonstration Data Archives

data.tar All Sample Data Below
valpha_all.tar All Sequential Assignment Data Below

Sample Data

apf.tar.Z 1D Batch Data
sample1d.tar.Z 1D Sample Data
sample2d.tar.Z 2D Sample Data
sample3d.tar.Z 3D Sample Data
cross.tar.Z Cross-Spectrum Data and Scripts
egg.tar.Z Sample NMR Image Data (Varian)
badnoe.tar.Z Example Replacement of Bad Planes in 3D Data Using LP
dosy.tar.Z DOSY-style 1D-Series (Pseudo-2D) Analysis
relax.tar.Z Pseudo-3D HN/N Relaxation Series Analysis
jmod.tar.Z Pseudo-3D J-Modulation Series Analysis
jc.tar.Z Pseudo-3D J-Modulation Series Analysis
jch.tar.Z Pseudo-4D J-Modulation Series Analysis
acme.tar.Z 2D COSY Data for ACME Coupling Constant Extraction
mag.tar.Z 2D Magnitude Mode (Absolute Value Mode) Example.
mem.tar.Z Maximum Entropy Reconstruction
gel.tar.Z Gel Image Converted to NMRPipe format and Quantified by 1D Lineshape Fitting
ipap.tar.Z Assignment and Analysis Example for 2D HN/N IPAP Data
sim3d.tar.Z Creation of Synthetic 3D Spectral Data
ubiqnoe.tar.Z 3D Sample Data, 3D 15N NOE of Ubiquitin
cbcaconh.tar.Z Examples of 3D Processing, Including MEM, ML, LP, and PCA-LP,
nusdemo2d.tar.Z Examples of 2D Non-Uniform Sampling (NUS) Reconstruction Using MEM and Maximum Liklihood
nusdemo3d.tar.Z Examples of 3D Non-Uniform Sampling (NUS) Reconstruction Using MEM and Maximum Liklihood

Data for Sequential Assignment

valpha.tar V-Alpha Protein, Triple Resonance Spectra
valpha_hn.tar V-Alpha Protein, 2D HN/N Data and Tables for Strip Viewer
valpha_time.tar V-Alpha Protein, Triple Resonance Time-Domain Data

Development Files

xview32_mac.tarXView Library for Mac OS X


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last updated:  Oct 14, 2016 / big fd