Resonance Assignment/AutoAssign - Revision history

Admin at 17:59, 16 December 2010

2010-12-16T17:59:27Z

← Older revision		Revision as of 17:59, 16 December 2010
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	*One can open a dataset to analyze start from the main menu by selecting <code>File+ -> =Open Control File</code> menu option or pressing the <code>Open Control File</code> button on the 4th tab (dataset completion) of the Dataset Creation Graphical User Interface.		*One can open a dataset to analyze start from the main menu by selecting <code>File+ -> =Open Control File</code> menu option or pressing the <code>Open Control File</code> button on the 4th tab (dataset completion) of the Dataset Creation Graphical User Interface.
	*~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~AutoAssign ~~AutoAssign]~~ will bring up the following window prompting the user to connect to a server (Figure 8):<br>		*AutoAssign will bring up the following window prompting the user to connect to a server (Figure 8):<br>

	==== Figure 8: Connection to Server ====		==== Figure 8: Connection to Server ====
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	*Next a blank <code>Connectivity Map</code> window is opened (Figure 9).		*Next a blank <code>Connectivity Map</code> window is opened (Figure 9).

	==== Figure 9:  Connectivity Map ====		==== Figure 9:  Connectivity Map ====

	=== Starting a Backbone Resonance Assignment ===		=== Starting a Backbone Resonance Assignment ===

Agutmana: moved AutoAssign to Resonance Assignment/AutoAssign

2010-01-05T22:51:40Z

moved AutoAssign to Resonance Assignment/AutoAssign

← Older revision	Revision as of 22:51, 5 January 2010
(No difference)

Jma at 02:43, 10 November 2009

2009-11-10T02:43:39Z

← Older revision		Revision as of 02:43, 10 November 2009
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	[[Image:Autoassign10.jpg]]		[[Image:Autoassign10.jpg]]

	<br>

			=== Assignment Constraints<br> ===

			The user can specify a variety of assignment constraints in the Notes column of a Sparky peak list using a controlled vocabulary.  These assignment constraints include: spin system typing, grouping and mapping constraints which are used by AutoAssign in the assignment process.  A complete description of assignment constraints and their usage in AutoAssign is provided in the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/preparing_datasets.html#Assignment_Constraints online documentation].

	=== '''Examining and Saving the Resonance Assignment Results''' ===		=== '''Examining and Saving the Resonance Assignment Results''' ===
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	*sparkyRL2bmrb.pl- converts Sparky resonance list into a BMRB file.		*sparkyRL2bmrb.pl- converts Sparky resonance list into a BMRB file.

			<br>

	== '''References'''<br> ==		== '''References'''<br> ==
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	-- GaohuaLiu - 11 Jun 2007		-- GaohuaLiu - 11 Jun 2007

	-- Updated/Edited by JimAramini - 09 Nov 2009		-- Updated/Edited by JimAramini - 09 Nov 2009

Jma at 02:16, 10 November 2009

2009-11-10T02:16:02Z

← Older revision		Revision as of 02:16, 10 November 2009
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	[http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html AutoAssign] is a constraint-based expert system for automating the assignment and analysis of backbone NMR resonance assignments of proteins (Ref. 1,2).  The program is implemented in C++, Java2, and Perl programming languages and supported on  SGI-IRIX, Sun-Solaris, MAC-OSX, x86-Linux, and x86_64-Linux architectures. The newest AutoAssign distribution (version 2.4.0) automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples.  The rich graphical user interface (GUI) provides a many sets of tools for dataset conversions, assignment validations, and various graphical displays of assignment results.  AutoAssign is well tested on a large number of independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~32 kD, including one fully-deuterated protein and and a dataset with reduced-dimensionality experiments.  AutoAssign performs the automated analysis of assignments in only seconds on current RISC and x86 platforms.		[http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html AutoAssign] is a constraint-based expert system for automating the assignment and analysis of backbone NMR resonance assignments of proteins (Ref. 1,2).  The program is implemented in C++, Java2, and Perl programming languages and supported on  SGI-IRIX, Sun-Solaris, MAC-OSX, x86-Linux, and x86_64-Linux architectures. The newest AutoAssign distribution (version 2.4.0) automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples.  The rich graphical user interface (GUI) provides a many sets of tools for dataset conversions, assignment validations, and various graphical displays of assignment results.  AutoAssign is well tested on a large number of independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~32 kD, including one fully-deuterated protein and and a dataset with reduced-dimensionality experiments.  AutoAssign performs the automated analysis of assignments in only seconds on current RISC and x86 platforms.

	The following description is mainly taken from the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign SOP (tutorial)].  Please check this tutorial and the version 2.4.0 [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/index.html help documentation] for more information and usage. <br>		The following description is mainly taken from the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign SOP (tutorial)].  Please check this tutorial and the version 2.4.0 [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/index.html help documentation] for more information and usage. <br>

	== '''Using AutoAssign''' ==		== '''Using AutoAssign''' ==
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	:		:
	145 9.153 112.004 57.415 2788050 HNCA </pre>		145 9.153 112.004 57.415 2788050 HNCA </pre>
	where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.		where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.

	== '''Performing Resonance Assignments''' ==		== '''Performing Resonance Assignments''' ==
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	#There are several options under <code>Save</code> -> <code>Chemical Shifts<span style="font-family: sans-serif;"> for saving the assignments in bmrb formats (2.1 and 3.0) and connectivity map format (cmap).</span></code><code><span style="font-family: sans-serif;" /></code><code><span style="font-family: sans-serif;" /></code><br><code></code>		#There are several options under <code>Save</code> -> <code>Chemical Shifts<span style="font-family: sans-serif;"> for saving the assignments in bmrb formats (2.1 and 3.0) and connectivity map format (cmap).</span></code><code><span style="font-family: sans-serif;" /></code><code><span style="font-family: sans-serif;" /></code><br><code></code>

			<br>

	== '''The Connectivity Map Image Editor''' ==		== '''The Connectivity Map Image Editor''' ==
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	==== Figure 11:  A CMap Image ====		==== Figure 11:  A CMap Image ====

	[[Image:Cmap image editor.gif]]		[[Image:Cmap image editor.gif]]

			== '''AutoPeak Scripts''' ==

			The AutoAssign bin directory features a plethora of perl scripts written by Hunter Moseley for many functions related to AutoAssign and its interplay with various programs including Sparky, as well as interconversion between a variety of formats.  A [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/PerlScripts.html glossary] of these scripts is available and a more in-depth description of the more commonly used scripts in our structure determination process is available [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/MajorUsesOfAutoPeak.html here].  Included among the major applications of the AutoPeak scripts is the creation and manipulation of chemical shift files in BMRB format.  Note that AutoPeak scripts in AutoAssign versions above 1.15.1 are written for BMRB 3.0 format. Here is a list of the scripts we most often use in our structure determinations:

			*bmrb2cmap.pl - converts bmrb format to cmap format. bmrbACS2SparkyPks.pl - converts bmrb assigned chemical shift save frame to Assigned Sparky Peak List format.
			*bmrb2AutoStructure.pl - converts bmrb format to AutoStructure Resonance List format.
			*compare_bmrb.pl - compares two bmrb files and returns how well they match.
			*missing_shifts.pl - reports the missing AtomTypes in a given BMRB file.
			*sparkyPks2bmrb.pl - converts a sparky peaklist into a BMRB assigned peak list save frame.
			*sparkyRL2bmrb.pl- converts Sparky resonance list into a BMRB file.



	== ~~<br>~~ '''References'''<br> ==		== '''References'''<br> ==

	1.   Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M.,  Shimotakahara, S., Chien, C., Powers, R. and Montelione, G.T. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. ''J. Mol. Biol. 269'', 592-610. <br>		1.   Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M.,  Shimotakahara, S., Chien, C., Powers, R. and Montelione, G.T. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. ''J. Mol. Biol. 269'', 592-610. <br>

	2.   Moseley, H.N.B., Monleon, D. and Montelione, G.T. (2001)  Automatic Determination of Protein Backbone Resonance Assignments from Triple Resonance NMR Data. ''<span style="font-style: italic;">Methods		2.   Moseley, H.N.B., Monleon, D. and Montelione, G.T. (2001)  Automatic Determination of Protein Backbone Resonance Assignments from Triple Resonance NMR Data. ''<span style="font-style: italic;">Methods</span>'' Enzymology 339'', 91-108.''
	~~Enzymology~~</span> 339'', 91-108.

	<br>		<br>

Jma at 19:50, 9 November 2009

2009-11-09T19:50:15Z

← Older revision		Revision as of 19:50, 9 November 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html AutoAssign] is a constraint-based expert system for automating the assignment and analysis of backbone NMR resonance assignments of proteins (Ref. 1).  The program is implemented in C++, Java2, and Perl programming languages and supported on  SGI-IRIX, Sun-Solaris, MAC-OSX, x86-Linux, and x86_64-Linux architectures. The newest AutoAssign distribution (version 2.4.0) automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples.  The rich graphical user interface (GUI) provides a many sets of tools for dataset conversions, assignment validations, and various graphical displays of assignment results.  AutoAssign is well tested on a large number of independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~32 kD, including one fully-deuterated protein and and a dataset with reduced-dimensionality experiments.  AutoAssign performs the automated analysis of assignments in only seconds on current RISC and x86 platforms.		[http://www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html AutoAssign] is a constraint-based expert system for automating the assignment and analysis of backbone NMR resonance assignments of proteins (Ref. 1,2).  The program is implemented in C++, Java2, and Perl programming languages and supported on  SGI-IRIX, Sun-Solaris, MAC-OSX, x86-Linux, and x86_64-Linux architectures. The newest AutoAssign distribution (version 2.4.0) automates the assignments of HN, NH, CO, CA, CB, HA, and HB resonances in non-, partially-, and fully-deuterated samples.  The rich graphical user interface (GUI) provides a many sets of tools for dataset conversions, assignment validations, and various graphical displays of assignment results.  AutoAssign is well tested on a large number of independently-collected triple-resonance NMR data sets of proteins ranging in size from ~6 to ~32 kD, including one fully-deuterated protein and and a dataset with reduced-dimensionality experiments.  AutoAssign performs the automated analysis of assignments in only seconds on current RISC and x86 platforms.

	The following description is mainly taken from the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign SOP (tutorial)].  Please check this tutorial and the version 2.4.0 [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/index.html help documentation] for more information and usage. <br>		The following description is mainly taken from the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign SOP (tutorial)].  Please check this tutorial and the version 2.4.0 [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/index.html help documentation] for more information and usage. <br>

	== '''Using AutoAssign''' ==		== '''Using AutoAssign''' ==

Jma at 19:49, 9 November 2009

2009-11-09T19:49:52Z

← Older revision		Revision as of 19:49, 9 November 2009
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	1.   Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M.,  Shimotakahara, S., Chien, C., Powers, R. and Montelione, G.T. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. ''J. Mol. Biol. 269'', 592-610. <br>		1.   Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M.,  Shimotakahara, S., Chien, C., Powers, R. and Montelione, G.T. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. ''J. Mol. Biol. 269'', 592-610. <br>

			2.   Moseley, H.N.B., Monleon, D. and Montelione, G.T. (2001)  Automatic Determination of Protein Backbone Resonance Assignments from Triple Resonance NMR Data. ''<span style="font-style: italic;">Methods
			Enzymology</span> 339'', 91-108.

			<br>

			<br>

			-- GaohuaLiu - 11 Jun 2007
	-- GaohuaLiu - 11 Jun 2007

	-- Updated/Edited by JimAramini - 09 Nov 2009		-- Updated/Edited by JimAramini - 09 Nov 2009

Jma at 19:45, 9 November 2009

2009-11-09T19:45:39Z

← Older revision		Revision as of 19:45, 9 November 2009
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	=== Manually Preparation of Peak Files (UB)<br> ===		=== Manually Preparation of Peak Files (UB)<br> ===

	One can manually prepare input files by using the follow format, [[UBNMR\|UBNMR]] can also be used to prepare the input files for AutoAssign. ''In [[UBNMR\|UBNMR ]]run <code>makeAutoList</code> to generate input files for AutoAssign.''		One can manually prepare input files by using the follow format, [[UBNMR\|UBNMR]] can also be used to prepare the input files for AutoAssign. ''In [[UBNMR\|UBNMR]] run <code>makeAutoList</code> to generate input files for AutoAssign.''

	<br>		<br>
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	...		...
	*		*
	</pre>		</pre>
	*Here is an example HNCA peak list file: <br>		*Here is an example HNCA peak list file: <br>
	<pre> #Index Xppm Yppm Zppm Intensity Label.notes		<pre> #Index Xppm Yppm Zppm Intensity Label.notes
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	125 8.870 110.898 62.529 724463 HNCA.;g45		125 8.870 110.898 62.529 724463 HNCA.;g45
	73 8.744 116.161 56.614 2287600 HNCA		73 8.744 116.161 56.614 2287600 HNCA
	:		:
	:		:
	145 9.153 112.004 57.415 2788050 HNCA </pre>		145 9.153 112.004 57.415 2788050 HNCA </pre>
	where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.		where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.

Jma at 19:45, 9 November 2009

2009-11-09T19:45:00Z

← Older revision		Revision as of 19:45, 9 November 2009
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	=== Manually Preparation of Peak Files (UB)<br> ===		=== Manually Preparation of Peak Files (UB)<br> ===

	One can manually prepare input files by using the follow format, [[UBNMR\|UBNMR]] can also be used to prepare the input files for AutoAssign. ''In [~~http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/~~UBNMR UBNMR] run <code>makeAutoList</code> to generate input files for AutoAssign.''		One can manually prepare input files by using the follow format, [[UBNMR\|UBNMR]] can also be used to prepare the input files for AutoAssign. ''In [[UBNMR\|UBNMR ]]run <code>makeAutoList</code> to generate input files for AutoAssign.''

	<br>		<br>

	*Peak File Format: ~~<br>~~ <pre><Index> <dim1> <dim2> [dimX] <Intensity> <Label>[.PeakNotes]		*Peak File Format:
	...</pre>		<pre> <Index> <dim1> <dim2> [dimX] <Intensity> <Label>[.PeakNotes]
			...
	*Here is an example HNCA peak list file: <br><pre> #Index Xppm Yppm Zppm Intensity Label.notes		*
	126 8.871 110.859 50.247 3242120 HNCA		</pre>
	125 8.870 110.898 62.529 724463 HNCA.;g45		*Here is an example HNCA peak list file: <br>
	73 8.744 116.161 56.614 2287600 HNCA		<pre> #Index Xppm Yppm Zppm Intensity Label.notes
	:		126 8.871 110.859 50.247 3242120 HNCA
	:		125 8.870 110.898 62.529 724463 HNCA.;g45
	145 9.153 112.004 57.415 2788050 HNCA </pre>where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.~~<span class="editHelp" />~~		73 8.744 116.161 56.614 2287600 HNCA
			:
			:
			145 9.153 112.004 57.415 2788050 HNCA </pre>
			where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.

	== '''Performing Resonance Assignments''' ==		== '''Performing Resonance Assignments''' ==

Jma at 19:43, 9 November 2009

2009-11-09T19:43:02Z

← Older revision		Revision as of 19:43, 9 November 2009
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	*Peak File Format: <br> <pre><Index> <dim1> <dim2> [dimX] <Intensity> <Label>[.PeakNotes]		*Peak File Format: <br> <pre><Index> <dim1> <dim2> [dimX] <Intensity> <Label>[.PeakNotes]
	</pre>		...</pre>

	~~...~~		*Here is an example HNCA peak list file: <br><pre> #Index Xppm Yppm Zppm Intensity Label.notes
			126 8.871 110.859 50.247 3242120 HNCA
	*

	*Here is an example HNCA peak list file: <br> <pre> #Index Xppm Yppm Zppm Intensity Label.notes
	~~</pre>~~

	126 8.871 110.859 50.247 3242120 HNCA
	125 8.870 110.898 62.529 724463 HNCA.;g45		125 8.870 110.898 62.529 724463 HNCA.;g45
	73 8.744 116.161 56.614 2287600 HNCA		73 8.744 116.161 56.614 2287600 HNCA
	~~ ~~:		:
	~~ ~~:		:
			145 9.153 112.004 57.415 2788050 HNCA </pre>where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.<span class="editHelp" />
	145 9.153 112.004 57.415 2788050 HNCA <br> where individual fields are separated by spaces and/or tabs, and comments are indicated by a "#" sign at the beginning of a line.

	== '''Performing Resonance Assignments''' ==		== '''Performing Resonance Assignments''' ==

Jma at 19:41, 9 November 2009

2009-11-09T19:41:24Z

← Older revision		Revision as of 19:41, 9 November 2009
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	== '''The Connectivity Map Image Editor''' ==		== '''The Connectivity Map Image Editor''' ==

	A connectivity map image represents resonance and other experimental data on the protein sequence in a graphical form.  The CMap Image Editor allows one to create such an image (Figure 11).  This facility is particularly useful for generating cmap images for publication.  For a complete description of this editor and all of its functions see the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html on-line documentation].		A connectivity map image represents resonance and other experimental data on the protein sequence in a graphical form.  The CMap Image Editor (which can be launched under the Tools tab) allows one to create such an image (Figure 11).  This facility is particularly useful for generating cmap images for publication.  For a complete description of this editor and all of its functions see the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html on-line documentation].

	==== Figure 11:  A CMap Image ====		==== Figure 11:  A CMap Image ====

	[[Image:~~Cmap_image_editor~~.gif]]		[[Image:Cmap image editor.gif]]

	== <br> '''References'''<br> ==		== <br> '''References'''<br> ==