What is it?
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.
NMRPipe is free and requires no licensing.
NMRDraw is the graphical interface to NMRPipe.
Note: these instructions are derived from the NMRPipe site: http://spin.niddk.nih.gov/NMRPipe/install/
Also note that the above site includes instructions for installing NMRPipe for Linux and Windows. The OS X instructions are somewhat lacking, thus this document.
Assumptions: this doc assumes you have basic knowledge of the OS X command line (terminal app) and of VI.
Install X11 type functionality
Download and install XQuartz from www.xquartz.org
Make sure you’re using the C-shell
NMRPipe/Draw requires the use of the C-shell or the T-shell (TENEX C Shell)
In a terminal window, type chsh (change shell; note that this command uses Vi editing commands).
The first line of the file will look something like this:
Shell: /bin/bash
Change it to this:
Shell: /bin/csh or
Shell:/bin/tcsh if you prefer the t-shell
Create a .cshrc file
To make sure you are at the root of your home folder, type: cd ~
Then type: touch .cshrc
Create the file structure for NMRPipe
Create an NMRPipe folder within your file system where you want NMRPipe to live. It is suggested that you put NMRPipe in the Applications folder.
Left-click on the Applications folder, then select “New Folder” from the File menu. Rename it to NMRPipe. Or if you’re using the Terminal app:
cd /Applications
mkdir NMRPipe
Files to download:
Links to these files are available on the NMRPipe website (http://spin.niddk.nih.gov/NMRPipe/install/).
- NMRPipeX.tZ
- install.com
- binval.com
- plugin.smile.tZ
- talos.tZ
- dyn.tZ
- NMRPipeL.tZ
Use the Finder to move these files from wherever they were downloaded to the NMRPipe folder created in step 2.
Tidy up the downloaded files and set permissions
1. Using the Terminal, type:
cd /Applications/NMRPipe
ls -l (to verify that the files from step 3 are in the folder)
2. Depending on what software is installed on the Mac, install.com and binval.com may have had .exe appended to the filename. To fix this, in the terminal type:
mv install.com.exe install.com
mv binval.com.exe binval.com
3. Set permissions on the files so the install will succeed. In the terminal, type:
chmod a+r *.tZ
chmod a+rx *.com
Install and Finalize
1. Install: in the terminal type:
./install.com
When the install completes, the following output will be dumped to the screen:
In order to use NMRPipe, users must first execute an
initialization script, for instance by adding these
lines to the end of their .cshrc file:
if (-e /Applications/nmrPipe/com/nmrInit.mac.com) then
source /Applications/nmrPipe/com/nmrInit.mac.com
endif
In order to use DYNAMO options, users must first execute
an initialization script, for instance by adding these
lines to their .cshrc file after NMRPipe initialization:
if (-e /Applications/nmrPipe/dynamo/com/dynInit.com) then
source /Applications/nmrPipe/dynamo/com/dynInit.com
endif
Mac OS X Users may also need to adjust X11 Preferences:
Under Windows Tab, Checkbox ON For:
x Click through Inactive Windows
x Focus Follows Mouse
x Focus on New Windows
If the nmrDraw graphical application does not run, users
might also need to execute the font initialization script:
if (-e /Applications/nmrPipe/com/font.com) then
source /Applications/nmrPipe/com/font.com
endif
NOTE: RESTART the computer after installing software, adjusting
configurations, or changing the .cshrc file.
2. Before you do anything with the output, check your .cshrc file:
- Type: more ~/.cshrc
- If you previously DID NOT have a .cshrc file, the install process may well have created one for you and populated it with the proper initialization scripts as described in Section A, above
- If you had a .cshrc file or it wasn’t populated during the install process, you’ll need to insert the appropriate if statements from Section A, above.
- Type: source .cshrc
3. Logout and back in
Test the Install (optional)
In a terminal, type one or more of the following commands:
which nmrPipe (Check that programs can be found)
nmrPipe -help (Run program in help mode)
man nmrPipe (Check manual pages)
bruker (Run the graphical conversion interface)
Run the App
nmrDraw (Launches the graphical interface)
Example .cshrc
#!/bin/csh
setenv PATH "${PATH}:/Applications/ccpnmr/bin/ /Applications/Sparky.app/Contents/Resources/bin/"
#
# Echo NMRPipe .cshrc commands created on Fri May 20 15:52:51 MDT 2016
# Echo see file /Applications/NMRPipe/README_NMRPIPE_USERS for more.
if (-e /Applications/NMRPipe/com/nmrInit.mac.com) then
source /Applications/NMRPipe/com/nmrInit.mac.com
endif
if (-e /Applications/NMRPipe/dynamo/com/dynInit.com) then
source /Applications/NMRPipe/dynamo/com/dynInit.com
endif
# if (-e /Applications/NMRPipe/com/font.com) then
# source /Applications/NMRPipe/com/font.com
# endif