NMRPipe General Installation Notes

NMRPipe Installation Guide
December 4, 2011

NMRPipe is an extensive software system for processing, analyzing, and exploiting NMR spectroscopic data.

More information about NMRPipe can be found at the NIH NMRPipe web site, and at the web site of NMRPipe's author, Frank Delaglio delaglio@nmrscience.com:

   http://spin.niddk.nih.gov/NMRPipe
   http://www.nmrscience.com

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/subscribe.cgi/nmrpipe

Some versions of NMRPipe may have expiration dates. To override the expiration date, use the following environment variable setting: 

     setenv NMR_CONT CORRECT_ALL

The following are GENERAL REQUIREMENTS for installing and using NMRPipe:

A typical installation of NMRPipe provides the following features and versions:

NMRPipe Installation Files

Use care when downloading NMRPipe installation files; 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. Also, some web browsers will not request and transmit the username and password required to download files from the list below. 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. Typical examples of the install files and sizes in use at the time of this writing are given below.

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 Dec 4, 2011 120,541,551 bytes NMRPipe programs for all systems (Version 6.2 Rev 2011.314.15.12)
   File 2 install.com Yes Dec 4, 2011 40,299 bytes Install script
   File 3 binval.com Yes Dec 4, 2011 3,807 bytes Used by install script
   File 4 talos.tZ No Dec 4, 2011 56,670,835 bytes Files required for TALOS+
   File 5 dyn.tZ No Dec 4, 2011 153,193,817 bytes Optional Ramachandran surfaces for TALOS+, PDB data and all files for DYNAMO and MFR
   File 6 s.tZ No Dec 4, 2011 186,283 bytes com Update with Special Scripts for 1D and 2D Screening, PCA, etc.

Special Note for TALOS Users

There is an improved replacement for TALOS, called TALOS+ ... this enhanced version provides a larger number of useful backbone angle predictions, 88% of residues in a given protein on average. TALOS+ is used in much the same way as earlier versions of TALOS. When the talos.tZ file is included during the NMRPipe install procedure, TALOS+ will be installed. The older version of TALOS will also be installed for backward-compatibility.

Introduction to Installation of NMRPipe

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

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:

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 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:


  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.

  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:


  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

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:

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 ..."

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 \
                 xorg-x11-fonts-75dpi  xorg-x11-fonts-ISO8859-1-75dpi  \
                 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 XVier 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:

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:

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 if needed)
   (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

The PC Linux version of NMRPipe has become especially popular, and it currently has the best processing and analysis benchmarks for any hardware.

There are currently two linux versions of NMRPipe, version linux and version linux9. The install procedure will automatically choose the NMRPipe Linux version is suitable, so that NMRPipe can be installed on most versions of Linux currently in use.

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. 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

When using graphical programs in the NMRPipe system, also note that all versions of the software expect use of a three-button scroll-wheel 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".

Lately, some 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

As noted previously, certain system details might cause Linux versions of nmrDraw to run slowly or not at all, or cause other graphics application problems such as distortions in the TALOS+ Ramachandran display. See the section NMRDRAW RUNS SLOWLY, OR NOT AT ALL above for more about these problems and potential solutions.

Also, 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 \ 
                 xorg-x11-fonts-75dpi  xorg-x11-fonts-ISO8859-1-75dpi  \
                 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

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), but will generally work on systems with higher versions of glibc. The linux9 version of NMRPipe is built under Fedora Core 9, and uses glibc 2.8. The install.com script will attempt to automatically determine which version is suitable for the given system. The default version is linux.

If you are not sure whether NMRPipe will run on your version of Linux, we recommend that you simply try the usual NMRPipe installation procedure first. Then, if you believe you need a version of NMRPipe for some other version of glibc, etc, write to the author Frank Delaglio at delaglio@nmrscience.com with your information.

When running the install script, a particular 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 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 at the NMRPipe download page.