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Jul 17, 2024, 6:05:29 AM7/17/24

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NMRPipe is an extensive software system for processing, analyzing, and exploiting multidimensional NMR spectroscopic data. This site contains NMRPipe installation files, as well as demo data with example processing andanalysis schemes for conventional and Non-Uniformly Sampled (NUS) spectra.

Important Note for Mac Users: Mac OS X no longer supports 32-bit applications,so that NMRPipe's graphical interface nmrDraw will not work on Mac OS X. A replacement for nmrDraw is underdevelopment. Likewise, while some versions of Windows include a Linux environment, the recommended solution for Windows systems is to install a Linux Virtual Machine.Depending on which installation files are used, the NMRPipe installation procedure provides the following features and versions:

Adobe Flash Player Error Could Not Load Curl Library Linux

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When downloading software from this web site, you are agreeing toour Terms of Use, including the termsthat there is no right to privacy on this system, and that thethe 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 thefiles, or use a different web browser if possible.

As an alternative to downloading via a web browser, on linux systems with the command wget available, you can downloadinstall files as needed. The wget command will not overwrite existing files,so be sure to delete any previous downloads first, for example:

If you are re-intalling NMRPipe, do a clean re-installation.This means renaming or deleting the existing installation,removing all NMRPipe initialization commands from the .cshrc filein your home directory, then deleting the .cshrc file if it has noother contents (it will be re-created by the install procedure). Be sure to log outand log in again before continuing with the new installation.

Use the +src option to install NMRPipe using *.tZ installation files that are stored in another directory, such as on a USB key. For example, if the *.tZ files are in a directory /media/USB16/pipefiles:

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 specific steps needed to install NMRPipe will differ dependingon 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 scriptswhich require read-write access. For this reason, it is oftenuseful to install "personal" copies of NMRPipe rather than install the software via the "root" account.

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 adjustedto read the installation files from some other source location, for example from a USB flash drive. 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 installfiles are stored together on the USB drive mounted as /media/USB16 andthe home directory is /Users/frank:

The installation procedure performs several software andgraphics tests to check the status of the installation. In somecases, these tests might issue warning messages even though theinstallation completes properly. In some cases, these testsmay fail in a way which interrupts the installation. If thishappens, you can suppress the post-installation software testswith the +nopost option, for example:

If you have an existing installation of NMRPipe, it must be removed or disabled before performinga new installation. This means you must remove any existing initialization commandsin the .cshrc file in your home directory, and log out before continuing.

Rename or delete the existing NMRPipe files. These are in the directorydefined by the environment variable $NMRBASE.
Remove any existing NMRPipe initialization commands from the .cshrcfile in your home directory. If the .cshrc contains only NMRPipeinitializations, you can rename it or delete it; when new versions of NMRPipe areinstalled, the install procedure will automatically create a suitable.cshrc file if one doesn't exist. The initialization commands inthe .cshrc will look something like this: if (-e /Users/nmruser/pipe/com/nmrInit.mac11_64.com) then source /Users/nmruser/pipe/com/nmrInit.mac11_64.com endif if (-e /Users/nmruser/pipe/dynamo/com/dynInit.com) then source /Users/nmruser/pipe/dynamo/com/dynInit.com endif if (-e /Users/nmruser/pipe/com/font.com) then source /Users/nmruser/pipe/com/font.com endif
Log out and log in again. This step is important, to insure thatnone of the old NMRPipe environment variable settings still exist,and that any previous NMRPipe font settings for graphics display are no longer active.

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 usethem in .cshrc will be listed in the file README_NMRPIPE_USERSwhich is also created during installation.

Also, regarding fonts: only use the "font.com" script if the "install.com" procedure orREADME_NMRPIPE_USERS file indicates thatit is needed for your system (mostly SGI/IRIX systems, andsome versions of Linux):

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 canbe adjusted by setting environment variables. Examples arelisted in the com/nmrInit.*.com file, and look like this:

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 "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.

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

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,