Mac OS X Installations for the NMRFAM Protein Structure

Mac OS X Installations for
the NMRFAM Protein
Structure Determination
Workshop
Table of Contents
Installing XQuartz on Mac OS X 10.8 or later ........................................................................... 1
Installing NMRFAM distribution of Sparky on Mac OS X ......................................................... 4
Installing MacPyMol on Mac OS X .......................................................................................... 8
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Installing XQuartz on Mac OS X 10.8 or later
As of OS X 10.8 (Mountain Lion), Apple no longer includes a X Window application so if you are
using OS X 10.8 or later, you must install one. XQuartz is an open source X Window application that
can be found at http://xquartz.macosforge.org. We have included a version of this software in the flash
drive you have received.
ONLY INSTALL if you are using Mac OS X 10.8 (Mountain Lion) or later. Earlier versions of Mac
OS X already have a X Window application, and installing XQuartz on them may cause problems.
Determine which version of OS X you have installed
1. Click the apple symbol in the menu bar at the top left of the screen and select About This
Mac.
2. This will pop up a window that indicates which version of OS X you are running.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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3. If the version number is 10.8 or later, you must install XQuartz. If the version number is
10.4 to 10.7, skip to the installation of Sparky.
Find XQuartz in the Workshop folder
1. Double-click the workshop folder you have on your desktop.
2. You will find the XQuartz application in
Assignments_and_Structure/NMRFAM_Sparky_distribution as XQuartz-2.7.4.dmg.
3. Double-click on that dmg file.
Install XQuartz
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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1. Double-clicking the dmg file will open a new Finder window with one icon called
XQuartz.pkg. Double-click this file.
2. The window shown here should pop up. Press Continue and follow the instructions for
the installation procedure.
3. NOTE: You will need the password for your account to install this software. It will ask
you for this password during the installation.
Log Out or Restart
When the installation for XQuartz says it's finished, you will need to log out or restart your
computer so XQuartz can configure itself to be the default X Window application.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Installing NMRFAM distribution of Sparky
on Mac OS X
Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other
polymers. The original software was developed at UCSF and can be found at
http://www.cgl.ucsf.edu/home/sparky. The NMRFAM distribution of Sparky that you will be using
during the workshop has some additional features added to it that help in the protein assignment
process.
Find Sparky in the Workshop Folder
1. Find the NMRFAM distribution of Sparky in the workshop folder under
Assignments_and_Structure/NMRFAM_Sparky_distribution
2. If you are using Mac OS X 10.5 or later, double-click on the sparky-mac.tar.gz file. This
will unzip the file and make a new folder in this directory called sparky-mac.
3. Drag the contents of the sparky-mac folder to your desktop.
4. If you are using Mac OS X 10.4, double-click on the sparky-mac_tiger.tar.gz file. This
will unzip the file and the Sparky application will show up in this folder. Drag it to the
desktop.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Find and Open Sparky Configuration File
By default, when Sparky starts, it will set your home directory as the starting point to look
for projects and spectra. Unfortunately, if the project you are working on is located several
folders away, you will spend quite a bit of time navigating the folder tree. To minimize this,
you can set a different default directory in the sparky configuration file. For this workshop,
we will set the default directory to the location of the files we will be working on.
1. Right-click on the Sparky application you dragged to your desktop and select Show
Package Contents. This will pop open a new Finder window.
2. Find the sparky configuration file in Contents/Resources/bin. The configuration file is
called sparky.
3. Right-click on sparky and select Open With > Other.
4. This will pop open a window of your installed Applications. Find and select TextEdit,
which will open the sparky configuration file in TextEdit.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Edit Sparky Configuration File
1. To the open sparky configuration file in TextEdit, copy and paste the following line to
the position in the file indicated in the figure above: setenv SPARKYHOME
"$HOME/Desktop/workshop_2013/Assignments_and_Structure/Sparky_assignmen
t_projects/Sparky_Backbone_Project"
2. Save the file and close TextEdit.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Testing Sparky Configuration
1. Double-click on the Sparky application icon on your desktop.
2. You should only have two windows pop up. If you get a third window that is asking you
create missing directories, select No, close Sparky, and check the configuration file
again. NOTE: When Sparky starts, it looks for three folders in the default directory you
have set: Lists, Projects, and Save. If they are not present you will get the third window
popup asking you to create them. If you are starting a brand new project, this is useful.
However, since we already have set up a project for you, you should not see this
window.
3. Additionally, you can check that you are in the correct directory in Sparky by selecting
File > Project Open. You should see the backbone.proj file.
4. Close Sparky.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Installing MacPyMol on Mac OS X
PyMol (www.pymol.org) is a molecular visualization application that is useful for viewing and
analyzing 3D molecular structures.
Find MacPyMol and NMR Structure Tools scripts in Workshop
Folder
1. The MacPyMol application can be found in the workshop folder under
Assignments_and_Structure/pymol/UW_pymol_licensed. The program is zipped as
macpymol-1_2r3.zip.
2. The NMR Structure Tools scripts used in MacPyMol are found in the workshop folder
under Assignments_and_Structure/pymol. There are two files you will need called
pymolrc and nmr_structure_tools.py.
3. Keep this finder window open as you will need to come back to it.
Mac OS X Installations for the NMRFAM Protein
Structure Determination Workshop
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Install MacPyMol
1. Double-click the macpymol-1_2r3.zip file. This will unzip the file and place the
MacPyMol application in this folder.
2. Drag the MacPyMol icon onto your Desktop.
Install NMR Structure Tools into MacPyMol
1. Right-click on the MacPyMol application you just dragged to the Desktop and select
Show Package Contents, which will open a new finder window.
2. Copy (command-C) the pymolrc file from the workshop folder in the other finder
window and paste it (command-V) into the pymol folder in the new finder window.
3. Copy (command-C) the nmr_structure_tools.py file from the workshop folder in the
other finder window and paste it (command-V) into the pymol/scripts folder in the new
finder window.
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Structure Determination Workshop
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Check the Installation
1. Double-click the MacPyMol application on your desktop to start MacPyMol.
2. When MacPyMol starts, you should see text in the pymol terminal referring to
nmr_structure_tools.py. (See picture).
3. Close MacPyMol, you are good to go.
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Structure Determination Workshop
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