Menu Descriptions


Contents


File Menu

File Menu

 

Open Table File
open a table file and initializea new data set.
Save Text Window save the text in the main panel ofAutoAssign window.
Save Command History save all the commands in the command history
Connect to Server establish connection to running AutoServer.
Disconnect from Server disconnect from running AutoServer.
Debug On turn on echoing of Client/Server communication.
Debug Off turn off echoing of Client/Server communication.
Exit
disconnect from Server and exit Client.
 

Execute Menu



Execute Menu
 
Default Execution
execute predefined analysis
Refined Execution
execute predefined analysis
Single Stage execute a single analysis stage separately
Create Ladders designate initial chemical shifts
Match Unambiguous establish strongest links
Match Degenerate establish links using non-unique chemical shifts
Extend Segments use assigned stretches of residues to extend assignments
Match Weaker GSs add back weaker spin systems and establish links
Match Inconsistent not yet implemented
Reason By Elimination not yet implemented
Finish Assignments not yet implemented
Single SubStage  execute a single step of analysis
Match Cycle
Incremental Match
Constrain Segments
Update Probabilities
Macro open and run a macro
Kill Task  stop the current execution


Single Stage - The default stages of analysis can be invoked individually (normally not done) or in sequence by running "Default Execution".  "Default Execution" is a programmable macro that normally is set to run two iterations of each analysis stage.

Single SubStage - execute a single step of analysis.

Macro - run AutoAssign command macro file. Please see the Macro Help for information on how to write your own macros and for the list of macro commands.
Kill Task - kill running execution task.


Examine Menu




Examine Menu
 
Chemical Shifts
display assigned chemical shifts in various formats.
Specific GS popup a GS selector window with a list of features to examine for a specific generic spin system.
Specific Residue popup a Residue selector window with a list of features to examine for a specific residue.
Specific Spectrum popup a Spectrum selector window with list a list of features to examine for a specific spectrum.
All GSs
display chemical shifts for all spin systems.
Unassigned GSs display chemical shifts for all unassigned spin systems.
Assigned GSs display chemical shifts for all assigned spin systems.
Weak GSs display chemical shifts for all weaker spin systems.
Unassigned Segments display chemical shifts for spin systems linked in this segment, along with possible assignments of segment and joint probabilities.
Assigned Segments display names of the residues included in all assigned segments.
Side Chain NH Roots list root frequencies of all side chain spin systems.
Overlapped GS Roots list root frequencies of all overlapped spin systems.
Unassigned Residues list the amino acid sequence with unassigned positions designated.  The expected chemical shifts templates for unassigned sites are listed as well.  These are similar to the templates used in the "Single Stage - Extend Segments" option under the Execute Menu.
All Assignment Constraints
list all assignment constraints found in peak notes.
Error Assignment Constraints
list an erroneous assignment constraints found in peak notes.

Chemical Shifts - display/save the assigned chemical shifts in various formats.

Save Menu






Save Menu
 
Chemical Shifts
save assigned chemical shifts in various formats.
All GSs
save chemical shifts for all spin systems.
Unassigned GSs save chemical shifts for all unassigned spin systems.
Assigned GSs save chemical shifts for all assigned spin systems.
Weak GSs save chemical shifts for all weaker spin systems.
Unassigned Segments save chemical shifts for spin systems linked in this segment, along with possible assignments of segment and joint probabilities.
Assigned Segments save names of the residues included in all assigned segments.
Side Chain NH Roots save root frequencies of all side chain spin systems.
Overlapped GS Roots save root frequencies of all overlapped spin systems.
Unassigned Residues save the amino acid sequence with unassigned positions designated.  The expected chemical shifts templates for unassigned sites are listed as well.  These are similar to the templates used in the "Single Stage - Extend Segments" option under the Execute Menu.
All Assignment Constraints
save all assignment constraints found in peak notes.
Error Assignment Constraints
save an erroneous assignment constraints found in peak notes.
All Sparky Peaklists
save all peak lists in assigned Sparky peaklist format.
Specific Sparky Peaklist
save a specific peak list in assigned Sparky peaklist format.

Modify Menu


Modify Menu

Preferences Opens a Preferences window where the default options are set



Tools Menu


Tools Menu

Analyze Set of analysis tools
Command History Display/Hide list of previously executed commands.
Connectivity Map  Display the Connectivity Map Window.
Connectivity Map Image
Open the CMap Image Editor.
Empty Text Editor Open an empty text editor
Text Editor Open a text file in the text editor.



Analyze - set of analysis tools.
1. An ideal GS is created for each non-proline residue whose CO- and CA-ladders have only the expected Ca and Cb shifts for the preceding and current residues respectively. These ideal spin systems are then examined to determine their theoretical possible assignments, and the total number of possible GS assignments for all assignable residues is computed.

2. This total number of possible assignments (N) is then divided by n to obtain the average number of possible assignments per residue (N/n).

3. To obtain a measure of sequence degeneracy which is independent of sequence length, the average obtained in the previous step is again divided by n.

For example, consider a sequence of five identical residues: AAAAA. Here, all but the first residue are assignable, and each position has four possible GS assignments. Thus N = 4 + 4 + 4 + 4 = 16, and the average is just 16/4 = 4. Similarly, given a sequence of ten alanines, we would have N = 36, with an average of 9 possible assignments per residue. In both cases however, dividing again by n yields a value of 1, which is the theoretical maximum sequence degeneracy. More generally, the final sequence degeneracy computed this way will always fall between 0 and 1, and provides a rough measure of redundancy in the sequence independent of n.

The Command History Window - clicking on any command in this window will cause that text to be copied to the "command field" in the main window for further editing if desired. Once the command is ready to be executed, clicking on the "Execute" button next to this field or pressing <enter> submits the request to the server if this is a server command or executes it if this is a Client command.  One can save commands by clicking the "Save History" button or remove all the commands from the list by clicking "Clear History" button.

Graphs Menu


Graphs Menu

Scatter Plot Display two dimensional overlays of peak lists to see how well the peaks from the two lists overlap in the selected dimensions.
Histogram Draws a simple column chart reflecting the differences for the observed versus expected C-alpha chemical shifts for each assigned residue.





Help Menu


Help Menu

Help Opens the Help Documentation in a web browser.
Release Notes
Open the Release Notes for this version of AutoAssign in a web browser.