AutoAssign Tutorial

Tutorial Steps

  1. Installing AutoAssign
  2. Starting AutoAssign
  3. Creating a Dataset
  4. Performing Resonance Assignments
  5. Validating Results

1. Installing AutoAssign

Installing AutoAssign is very simple.  All you need to do is unzip-untar the distribution, and run the INSTALL script in the distribution.  The install script will prompt you for any pertinent information needed for the installation.   The user can usually select the defaults for most questions.  However, the location of Java is one that the user will normally have to specify.  Sun Microsystem's distribution of Java is required and is normally located in the directory /usr/java.   The following shows a standard installation performed as the root user:

[root@apollo junk20]# tar -xvzf autoassign-2.1.0.tar.gz
[root@apollo junk20]# cd autoassign-2.1.0/
[root@apollo autoassign-2.1.0]# pwd
[root@apollo autoassign-2.1.0]# ./INSTALL
Valid OS Types are Linux/Linux64/SunOS/IRIX/IRIX64/DARWIN(MAC_OSX).
Which version should be installed: [LINUX64]:

Where would you like the AutoAssign distribution installed: [/usr/local/AutoAssign2.1.0]:
/usr/local is a common place for 3rd party software to install in a Linux/Unix environment.

Found web browsers are:
Which web broswer should be used: [/usr/bin/firefox]:

Perl can be found at:
Which perl should be used: [/usr/bin/perl]:

Java can be found at:
Sun Java is normally located under /usr/java
Which java should be used: [/usr/bin/java]: /usr/java/jdk1.5.0_05/bin/java
This is the path to the Sun Java Virtual Machine executable.

creating /usr/local/AutoAssign2.1.0
Installing AutoServer...DONE
Installing AutoClient...DONE
Installing ExampleData files...DONE
Installing Documentation files...DONE
Installing Macros files...DONE
Installing filter files...DONE
Installing Scripts...DONE
Installing Executable files...DONE
Changing the file protection of the installed files...DONE
What computer should be the default server host: [apollo]:
What should the default port be (something > 3500): [8050]:
Where do you want temporary files put when running AutoAssign: [/tmp/]:
Creating the AutoAssign preference file...DONE
Creating  startup script...DONE
Creating autoserver startup script...DONE
Where would you like the startup scripts installed [/usr/local/bin]:
Installing autoclient startup script in /usr/local/bin ...DONE
Installing autoassign startup script in /usr/local/bin ...DONE
Installing autoserver startup script in /usr/local/bin ...DONE
Installing .AArc preference file in /usr/local/AutoAssign2.1.0 ...DONE
Who should own the installed files (use "none" not to change): [root.sys]:

You should now be ready to start AutoAssign using the autoassign and autoserver startup scripts.

2. Starting AutoAssign

If you are running the client on the same machine as the server, then you simply run the startup script "autoassign".  It will start a server for you if one is not running.

If you are running the client on a machine different from the server, then you must first make sure that the server is running on the other machine.  The easiest way to do this is to run the startup script "autoserver" on this other computer.  This script will start a server if one is not running and will print out the port numbers of servers that are running.  Then you can start the client on the first machine using the startup script as follows:

 % autoassign
No AutoServer detected on apollo. Starting new AutoServer on port 8050...
[1] 15341
Starting AutoClient...
AutoAssign 2.1.0
AutoAssign(c) 1997,2000,2006 H. Moseley, D. Zimmerman, C. Kulikowski, and G. Montelione.
[2] 15343

The main AutoAssign window will appear:

Main AutoAssign Window

3. Creating a Dataset

The easiest way to create a dataset is to using the Dataset Creation Graphical User Interface.  This interface will guide you through the basic steps of converting your peak lists, registering your peak lists, creating a control file, and evaluating the quality of your peak lists.  In particular, the Peak Lists Quality Assessment Report gives valuable information to guide the user in cleaning up and improving the raw peak lists.  Also, it would be good to look at the Experimental Assignment Strategies that AutoAssign can readily handle.  Once you have the raw peak lists needed for an assignment strategy, you can select the "Convert/Create Dataset" File menu option to start the Dataset Creation Graphical User Interface.

This will pull up the following window:

Dataset Creation GUI

Now follow the Dataset Creation process that the interface guides you through.  At the end, you will have a dataset in AutoAssign format ready for AutoAssign to analyze.

4. Performing Resonance Assignments

You now can open a dataset to analyze by selecting the "Open Control File" File menu option or pressing the "Open Control File" button on the 4th tab of the Dataset Creation Graphical User Interface.  This button is circled below:

Dataset Creation GUI Completion Tab

Next, AutoAssign will bring up the following window prompting the user to connect to a server.  If the client and server are on the same computer, you should be able to simply select "Connect".

Connect To Server

Now things brings up a blank ConnectivityMap Window.

Connectivity Map

Next, the user can select the "Default Execution" Execute menu option to start the analysis.  "Default Execution" is the suggested method to run the program.  The "Refined Execution" Execute menu option run AutoAssign in an aggressive mode which is not as safe as the "Default Execution" option.

Default Execution

The Connectivity Map will show the resonance assignment results as the analysis progresses.  The whole analysis should only take a few seconds.

Connectivity Map filled

The user can now examine and save the resonance assignment results in a human readable "Publish Format, 2.1 and 3.0 BMRB NMRStar formats, and Sparky Resonance List and Peak List formats.  These options can be selected under the Chemical Shift submenus of the Examine and Save menus.  The "Specific GS", "Unassigned Residues", and "Unassigned GSs" Examine menu options are very valuable to troubleshoot problems with assignments or missing assignments.  These can be as guides to reexamine spectra to find missing peaks or to apply peak-based assignment constraints if such interventions are necessary.

Examine Menu

5. Validating Results

When using any analysis tool, you need to validate your results.  This is true in any form of analysis, especially scietific analysis.  So, once you get the assignment results from AutoAssign, you need to validate the assignments.  AutoAssign provides Assignment Validation Software suite (AVS) to aid the user in validating assignments.  The four main tools in AVS are: