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Installing nmrPipe/Draw for OS X

Tags nmrpipe

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:

  1. Type:  more ~/.cshrc
  2. 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
  3. 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.
  4. 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

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Details

Article ID: 10897
Created
Tue 1/26/16 9:49 AM
Modified
Fri 4/7/17 8:49 AM