AGNuS/AutoProc - Revision history

Jma at 15:57, 5 October 2011

2011-10-05T15:57:30Z

← Older revision		Revision as of 15:57, 5 October 2011
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	</pre>		</pre>
	Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference a spectrum.  We reference to internal DSS in all of our production work.		Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference a spectrum.  We reference to internal DSS in all of our production work.  In a typical data production run collection we start with a 1D <sup>1</sup>H NMR spectrum and obtain the absolute resonance frequency of DSS under the conditions used for the NMR experiments.  This value is then used in the subsequent AutoProc processing of all fids from the data collection, as described below (option 7).

	In a typical data production run collection we start with a 1D <sup>1</sup>H NMR spectrum and obtain the absolute resonance frequency of DSS under the conditions used for the NMR experiments.  This value is then used

	in the subsequent AutoProc processing of all fids from the data collection, as described below (option 7).
	<pre>AGNuS 2.1		<pre>AGNuS 2.1
	Type "agnus -help" for help		Type "agnus -help" for help

Jma at 15:56, 5 October 2011

2011-10-05T15:56:50Z

← Older revision		Revision as of 15:56, 5 October 2011
Line 45:		Line 45:
	</pre>		</pre>
	Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference a spectrum.  We reference to internal DSS in all of our production work.		Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference a spectrum.  We reference to internal DSS in all of our production work.

			In a typical data production run collection we start with a 1D <sup>1</sup>H NMR spectrum and obtain the absolute resonance frequency of DSS under the conditions used for the NMR experiments.  This value is then used

			in the subsequent AutoProc processing of all fids from the data collection, as described below (option 7).
	<pre>AGNuS 2.1		<pre>AGNuS 2.1
	Type "agnus -help" for help		Type "agnus -help" for help

Jma at 16:52, 5 January 2010

2010-01-05T16:52:05Z

← Older revision		Revision as of 16:52, 5 January 2010
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	<br>		<br>

	<br>		<br>

	~~<br>~~

	~~-- GaohuaLiu - 31 May 2007~~

	~~-- Updated by JimAramini - 11 Nov 2009~~

Jma at 22:41, 11 November 2009

2009-11-11T22:41:25Z

← Older revision		Revision as of 22:41, 11 November 2009
Line 9:		Line 9:
	=== Processing a 2D <sup>1</sup>H,<sup>15</sup>N-HSQC Using AGNuS ===		=== Processing a 2D <sup>1</sup>H,<sup>15</sup>N-HSQC Using AGNuS ===

	AGNuS parses procpar (Varian) and acqu* (Bruker) files for spectral parameters.  The program consults a pulse sequence table specific to the sequence used in the ~~experiement~~.  For example, this is the table file for the standard Bruker 2D <sup>1</sup>H,<sup>15</sup>N-HSQC, hsqcetf3gpsi.  If the sequence table file is missing from the Pulse_Sequences directory in AGNuS, the program will ~~through~~ an error, and the user must create one (best to clone one from an similar one already in the directory).<br>		AGNuS parses procpar (Varian) and acqu* (Bruker) files for spectral parameters.  The program consults a pulse sequence table specific to the sequence used in the experiment.  For example, this is the table file for the standard Bruker 2D <sup>1</sup>H,<sup>15</sup>N-HSQC, hsqcetf3gpsi.  If the sequence table file is missing from the Pulse_Sequences directory in AGNuS, the program will throw an error and the user must create one (best to clone one from an similar one already in the directory).<br>
	<pre># This is a Bruker experiment and only a table for testing.		<pre># This is a Bruker experiment and only a table for testing.

Line 44:		Line 44:

	</pre>		</pre>
	Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference ~~the~~ spectrum.  We reference to internal DSS in all of our production work.		Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference a spectrum.  We reference to internal DSS in all of our production work.
	<pre>AGNuS 2.1		<pre>AGNuS 2.1
	Type "agnus -help" for help		Type "agnus -help" for help
Line 98:		Line 98:
	Absolute Frequency of DSS: 800.1899230		Absolute Frequency of DSS: 800.1899230
	</pre>		</pre>
	This produces the following NMRPipe conversion file, which the user then ~~can~~ modify and ~~subquently~~ run:		This produces the following NMRPipe conversion file, which the user can then modify and subsequently run:
	<pre>Conversion script:		<pre>Conversion script:
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line 122:		Line 122:
	Known Nuclei: H,N		Known Nuclei: H,N
	</pre>		</pre>
	A default NMRPipe processing script is then generated, which can again be modified by the user, and ~~subequently~~ run:		A default NMRPipe processing script is then generated, which can again be modified by the user, and subsequently run:
	<pre>Full Processing script:		<pre>Full Processing script:
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Jma at 22:38, 11 November 2009

2009-11-11T22:38:52Z

← Older revision		Revision as of 22:38, 11 November 2009
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	</pre>		</pre>
	Next the program launches NMRDraw.  Here the user determines phase corrections in both dimensions, which are then applied to the processing script and the data is reprocessed ~~(Figure 1)~~.		Next the program launches NMRDraw (Figure 1).  Here the user determines phase corrections in both dimensions, which are then applied to the processing script and the data is reprocessed.

	==== Figure 1: An NMRDraw Window for a <sup>1</sup>H,<sup>15</sup>N-HSQC ====		==== Figure 1: An NMRDraw Window for a <sup>1</sup>H,<sup>15</sup>N-HSQC ====

	[[Image:~~AGNuS_NMRDraw~~.png\|800px]]<br>		[[Image:AGNuS NMRDraw.png\|800px]]<br>

	Finally, the user converts to SPARKY or XEASY format, and proceeds to spectral analysis.		Finally, the user converts to SPARKY or XEASY format, and proceeds to spectral analysis.

Jma at 22:35, 11 November 2009

2009-11-11T22:35:09Z

← Older revision		Revision as of 22:35, 11 November 2009
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	== '''How to Use AGNuS''' ==		== '''How to Use AGNuS''' ==

	=== Processing a 2D <sup>1</sup>H,<sup>15</sup>N-HSQC Using AGNuS ===		=== Processing a 2D <sup>1</sup>H,<sup>15</sup>N-HSQC Using AGNuS ===

	AGNuS parses procpar (Varian) and acqu* (Bruker) files for spectral parameters.  The program consults a pulse sequence table specific to the sequence used in the experiement.  For example, this is the table file for the standard Bruker 2D <sup>1</sup>H,<sup>15</sup>N-HSQC, hsqcetf3gpsi.  If the sequence table file is missing from the Pulse_Sequences directory in AGNuS, the program will through an error, and the user must create one (best to clone one from an similar one already in the directory).<br>		AGNuS parses procpar (Varian) and acqu* (Bruker) files for spectral parameters.  The program consults a pulse sequence table specific to the sequence used in the experiement.  For example, this is the table file for the standard Bruker 2D <sup>1</sup>H,<sup>15</sup>N-HSQC, hsqcetf3gpsi.  If the sequence table file is missing from the Pulse_Sequences directory in AGNuS, the program will through an error, and the user must create one (best to clone one from an similar one already in the directory).<br>
	<pre># This is a Bruker experiment and only a table for testing.		<pre># This is a Bruker experiment and only a table for testing.

	file_type : single_fid_table		file_type : single_fid_table
	name : hsqcetf3gpsi		name : hsqcetf3gpsi
	nickname : HSQC		nickname : HSQC
	dimensions : [		dimensions : [
	nuclei : H		nuclei : H
	offset_parameter : O1_1		offset_parameter : O1_1
	acquisition_mode : DQD		acquisition_mode : DQD
	]		]
	dimensions : [		dimensions : [
	nuclei : N		nuclei : N
	offset_parameter : O1_2		offset_parameter : O1_2
	acquisition_mode : Echo-AntiEcho		acquisition_mode : Echo-AntiEcho
	]		]

	processing_defaults : [		processing_defaults : [
	name : "Sine Bell Default"		name : "Sine Bell Default"
	suffix : _SP		suffix : _SP
	dimensions :  [		dimensions :  [
	transformation : FT		transformation : FT
	apodization : "SP -off 0.45 -end 0.98 -pow 2"		apodization : "SP -off 0.45 -end 0.98 -pow 2"
	first_point_correction : 0.5		first_point_correction : 0.5
	phase0 : -60		phase0 : -60
	]		]
	dimensions :  [		dimensions :  [
	transformation : FT		transformation : FT
	apodization : "SP -off 0.45 -end 0.98 -pow 2"		apodization : "SP -off 0.45 -end 0.98 -pow 2"
	first_point_correction : 0.5		first_point_correction : 0.5
	phase0 : -90		phase0 : -90
	]		]
	]		]

	</pre>		</pre>
	Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference the spectrum.  We reference to internal DSS in all of our production work.		Start autoproc and enter a spectrometer, then a DSS value for referencing.  This is the most optimal way to reference the spectrum.  We reference to internal DSS in all of our production work.
	<pre>AGNuS 2.1		<pre>AGNuS 2.1
	Type "agnus -help" for help		Type "agnus -help" for help
Line 97:		Line 97:

	Absolute Frequency of DSS: 800.1899230		Absolute Frequency of DSS: 800.1899230
	</pre>		</pre>
	This produces the following NMRPipe conversion file, which the user then can modify and subquently run:		This produces the following NMRPipe conversion file, which the user then can modify and subquently run:
	<pre>Conversion script:		<pre>Conversion script:
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line 122:		Line 122:
	Known Nuclei: H,N		Known Nuclei: H,N
	</pre>		</pre>
	A default NMRPipe processing script is then generated, which can again be modified by the user, and subequently run:		A default NMRPipe processing script is then generated, which can again be modified by the user, and subequently run:
	<pre>Full Processing script:		<pre>Full Processing script:
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line 146:		Line 146:
	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

	</pre>		</pre>
	Next the program launches NMRDraw.  Here the user determines phase corrections in both dimensions, which are then applied to the processing script and the data is reprocessed (Figure 1).		Next the program launches NMRDraw.  Here the user determines phase corrections in both dimensions, which are then applied to the processing script and the data is reprocessed (Figure 1).

	~~==== Figure 1: An NMRDraw Window for a <sup>1</sup>H,<sup>15</sup>N-HSQC ====~~

	~~[[Image:AGNus_example_4.jpg\|800px]]~~



	~~Finally~~, ~~the user converts to SPARKY or XEASY format, and proceeds to spectral analysis.~~		==== Figure 1: An NMRDraw Window for a <sup>1</sup>H,<sup>15</sup>N-HSQC ====

			[[Image:AGNuS_NMRDraw.png\|800px]]<br>

			Finally, the user converts to SPARKY or XEASY format, and proceeds to spectral analysis.

	~~=== Processing a 3D Experiments Using AGNuS ===~~		<br>

	Processing ~~higher dimensionality experiments using AGNuS is essentially the same process with a few minor differences. For example, for~~ a 3D ~~experiment, the user first produces F1F3 (xy) and F2F3 (xz) 2D planes which are phase corrected using NMRDraw.  Then the 3D NMRPipe script is run to produce the 3D processed pipe file.~~		=== Processing a 3D Experiments Using AGNuS ===

			Processing higher dimensionality experiments using AGNuS is essentially the same process with a few minor differences. For example, for a 3D experiment, the user first produces F1F3 (xy) and F2F3 (xz) 2D planes which are phase corrected using NMRDraw.  Then the 3D NMRPipe script is run to produce the 3D processed pipe file.

			<br>

	=== '''Processing a GFT Experiment Using AGNuS''' ===		=== '''Processing a GFT Experiment Using AGNuS''' ===

Jma at 22:23, 11 November 2009

2009-11-11T22:23:54Z

Show changes

Jma at 21:46, 11 November 2009

2009-11-11T21:46:50Z

← Older revision		Revision as of 21:46, 11 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. AGNuS automatically generates NMRPipe scripts for processing multidimensional NMR experiments and provides functions for chemical referencing.  AGNuS calls information  for specific experiments and spectrometers stored in table files, which can be generated/modified by users with permission.  AGNuS is also capable of processing reduced dimensionality/GFT experiments.		[http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. AGNuS automatically generates NMRPipe scripts for processing multidimensional Varian or Bruker NMR experiments and provides functions for chemical referencing.  AGNuS calls information  for specific experiments and spectrometers stored in table files, which can be generated/modified by users with permission.  AGNuS is also capable of processing reduced dimensionality/GFT experiments.

	Please check [~~http~~:~~//www~~.~~nsm.buffalo.edu/Chem/HTP_twiki43/pub/NESG/AGNuS/agnus.html SOP of AGNuS~~] for addtional information ~~and examples of processing 2D and 3D NMR experiments~~.<br>		The current version of the program is AutoProc 2.0.  Please check the [[Media:AGNuS_help.jpg\|documentation]] and examples provided with the software for addtional information.<br>

	== '''How to Use AGNuS''' ==		== '''How to Use AGNuS''' ==
Line 9:		Line 9:
	== '''Processing a GFT Experiment''' ==		== '''Processing a GFT Experiment''' ==

	Here are some instructions for processing a GFT experiment:		Here are some instructions for processing a GFT experiment:

	Before running AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. The table files for the most used NMR experiments are availble from AGNuS. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>MULTI</code> for GFT basic experiments process.		Before running AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. The table files for the most used NMR experiments are availble from AGNuS. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>MULTI</code> for GFT basic experiments process.

Jma at 21:15, 11 November 2009

2009-11-11T21:15:16Z

Jma at 21:13, 11 November 2009

2009-11-11T21:13:07Z

← Older revision		Revision as of 21:13, 11 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	[http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. AGNuS automatically generates NMRPipe scripts for processing multidimensional NMR experiments and provides functions for chemical referencing.  AGNuS calls information  for specific experiments and spectrometers stored in table files, which can be generated/modified by users with permission.  AGNuS is also capable of processing reduced dimensionality/GFT experiments.		[http://www-nmr.cabm.rutgers.edu/software/autoproc.htm Autoproc/AGNuS] is a suite of programs for the automatic generation of scripts for multidimensional protein NMR data processing and format conversion. AGNuS automatically generates NMRPipe scripts for processing multidimensional NMR experiments and provides functions for chemical referencing.  AGNuS calls information  for specific experiments and spectrometers stored in table files, which can be generated/modified by users with permission.  AGNuS is also capable of processing reduced dimensionality/GFT experiments.

	Please check [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/pub/NESG/AGNuS/agnus.html SOP of AGNuS] for addtional information and examples of processing 2D and 3D NMR experiments.		Please check [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/pub/NESG/AGNuS/agnus.html SOP of AGNuS] for addtional information and examples of processing 2D and 3D NMR experiments.<br>
	==

	== '''How to Use AGNuS''' ==		== '''How to Use AGNuS''' ==

			== '''Processing a GFT Experiment''' ==

	== '''Processing a GFT Experiment''' ==

	Here are some instructions for processing a GFT experiment:<br>		Here are some instructions for processing a GFT experiment:<br>

			<br>

			*

	*		Before run AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. These table file of the most used NMR experiments are availble from AGNus. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>*MULTI</code> for GFT basic experiments process.
	Before run AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. These table file of the most used NMR experiments are availble from AGNus. ~~[http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/AGNuS~~ AGNuS] will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>*MULTI</code> for GFT basic experiments process.

	'''Example of pulse sequence table for GFT_43D_CABCAcoNHN'''		'''Example of pulse sequence table for GFT_43D_CABCAcoNHN'''
	<pre>file_type : single_fid_table		<pre>file_type : single_fid_table
	name : GFT_43D_CBCACAcoNHN		name : GFT_43D_CBCACAcoNHN
	nickname : HNcoCACB_GFT		nickname : HNcoCACB_GFT
	synonym : GFT_43D_CBCACAcoNHN_MULTI		synonym : GFT_43D_CBCACAcoNHN_MULTI
	dimensions : [		dimensions : [
	nuclei : H		nuclei : H
	offset_parameter : tof		offset_parameter : tof
	acquisition_mode : Complex		acquisition_mode : Complex
	]		]
	dimensions : [		dimensions : [
	nuclei : C		nuclei : C
	offset_parameter : dof		offset_parameter : dof
	acquisition_mode : Complex		acquisition_mode : Complex
	]		]
	dimensions : [		dimensions : [
	nuclei : N		nuclei : N
	offset_parameter : dof2		offset_parameter : dof2
	acquisition_mode : Complex		acquisition_mode : Complex
	]		]

	processing_defaults : [		processing_defaults : [
	name : "Sine Bell Default"		name : "Sine Bell Default"
	dimensions : [		dimensions : [
	transformation : FT		transformation : FT
	apodization : "SP -off 0.45 -end 0.98 -pow 2"		apodization : "SP -off 0.45 -end 0.98 -pow 2"
	first_point_correction : 0.5		first_point_correction : 0.5
	]		]
	dimensions : [		dimensions : [
	transformation : FT		transformation : FT
	apodization : "SP -off 0.45 -end 0.98 -pow 1"		apodization : "SP -off 0.45 -end 0.98 -pow 1"
	first_point_correction : 1.0		first_point_correction : 1.0
	]		]
	dimensions : [		dimensions : [
	transformation : "FT -neg"		transformation : "FT -neg"
	apodization : "SP -off 0.45 -end 0.98 -pow 1"		apodization : "SP -off 0.45 -end 0.98 -pow 1"
	first_point_correction : 0.5		first_point_correction : 0.5
	]		]
	xy_plane : 002		xy_plane : 002
	]</pre>		]</pre>
	*To run AGNus, simply go to the directory only contains the Varian fid and procpar (parameter) file; type <code>agnus</code> and follow the instructions prompted by AGNus. Type <code>agnus -help</code> for help.		*To run AGNus, simply go to the directory only contains the Varian fid and procpar (parameter) file; type <code>agnus</code> and follow the instructions prompted by AGNus. Type <code>agnus -help</code> for help.
	#Select <code>MULTI</code> for GFT basic experiments process (optional, AGNus will go to the next step if non-GFT data if identified)		#Select <code>MULTI</code> for GFT basic experiments process (optional, AGNus will go to the next step if non-GFT data if identified)
Line 68:		Line 66:
	*##Use <code>CTRL-C</code> to quit AGNus after phasing the spectrum with NMRDraw		*##Use <code>CTRL-C</code> to quit AGNus after phasing the spectrum with NMRDraw
	*##Rerun AGNus and manually type in or correct the phase when come to the process scripts change step. Modify the base line parameter as well if necessary		*##Rerun AGNus and manually type in or correct the phase when come to the process scripts change step. Modify the base line parameter as well if necessary
	*##Run the final process after all parameters be carefully reviewed.		*##Run the final process after all parameters be carefully reviewed.
	*#Run the UCSF conversion and cleanup script if use SPARKY for NMR data analysis. Run [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/SPSCAN SPSCAN] to conver Buffalo.NMRPipe format data to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] format data if use [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY].		*#Run the UCSF conversion and cleanup script if use SPARKY for NMR data analysis. Run [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/SPSCAN SPSCAN] to conver Buffalo.NMRPipe format data to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] format data if use [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY].

			<br>

			<br>

			<br>

			<br>

			<br>

			<br>






	-- GaohuaLiu - 31 May 2007		-- GaohuaLiu - 31 May 2007

	-- Updated by JimAramini - 11 Nov 2009		-- Updated by JimAramini - 11 Nov 2009

← Older revision		Revision as of 21:15, 11 November 2009
Line 9:		Line 9:
	== '''Processing a GFT Experiment''' ==		== '''Processing a GFT Experiment''' ==

	Here are some instructions for processing a GFT experiment:~~<br>~~		Here are some instructions for processing a GFT experiment:

	~~<br>~~		Before running AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. The table files for the most used NMR experiments are availble from AGNuS. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>MULTI</code> for GFT basic experiments process.

	*

	Before ~~run~~ AGNuS, an appropriate pulse sequence table corresponding to the NMR data should be prepared. ~~These~~ table ~~file of~~ the most used NMR experiments are availble from ~~AGNus~~. AGNuS will automatically detects the procpar file, parses it, and selects the appropriate parameters from the procpar and the corresponding experiment description (pulse sequence table). Select <code>*MULTI</code> for GFT basic experiments process.

	'''Example of pulse sequence table for GFT_43D_CABCAcoNHN'''		'''Example of pulse sequence table for GFT_43D_CABCAcoNHN'''
Line 57:		Line 53:
	xy_plane : 002		xy_plane : 002
	]</pre>		]</pre>
	*To run ~~AGNus~~, simply go to the directory only contains the Varian fid and procpar (parameter) file; type <code>agnus</code> and follow the instructions prompted by ~~AGNus~~. Type <code>agnus -help</code> for help.		*To run AGNuS, simply go to the directory only contains the Varian fid and procpar (parameter) file; type <code>agnus</code> and follow the instructions prompted by AGNuS. Type <code>agnus -help</code> for help.
	#Select <code>MULTI</code> for GFT basic experiments process (optional, ~~AGNus~~ will go to the next step if non-GFT data if identified)		#Select <code>MULTI</code> for GFT basic experiments process (optional, AGNuS will go to the next step if non-GFT data if identified)
	*#Selecting the spectrometer		*#Selecting the spectrometer
	*#Select the basic information about where files are located, name of conversion scripts, and names of converted files.		*#Select the basic information about where files are located, name of conversion scripts, and names of converted files.
	*#Run the conversion script provided by ~~AGNus~~ to convert NMR data format to Pipe format. Modify the conversion script is necessary.		*#Run the conversion script provided by AGNuS to convert NMR data format to Pipe format. Modify the conversion script is necessary.
	*#Run the process scripts (3D and XY, XZ planes process scripts for 3D data) provided by ~~AGNus~~. Modify the Buffalo.NMRPipe process parameters such as phase values if necessary.		*#Run the process scripts (3D and XY, XZ planes process scripts for 3D data) provided by AGNuS. Modify the Buffalo.NMRPipe process parameters such as phase values if necessary.
	*##~~AGNus~~ will lauch NMRDraw to let the user to check the process data and get the phase values.		*##AGNuS will lauch NMRDraw to let the user to check the process data and get the phase values.
	*##Use <code>CTRL-C</code> to quit ~~AGNus~~ after phasing the spectrum with NMRDraw		*##Use <code>CTRL-C</code> to quit AGNuS after phasing the spectrum with NMRDraw
	*##Rerun ~~AGNus~~ and manually type in or correct the phase when come to the process scripts change step. Modify the base line parameter as well if necessary		*##Rerun AGNuS and manually type in or correct the phase when come to the process scripts change step. Modify the base line parameter as well if necessary
	*##Run the final process after all parameters be carefully reviewed.		*##Run the final process after all parameters be carefully reviewed.
	*#Run the UCSF conversion and cleanup script if use SPARKY for NMR data analysis. Run [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/SPSCAN SPSCAN] to conver Buffalo.NMRPipe format data to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] format data if use [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY].		*#Run the UCSF conversion and cleanup script if use SPARKY for NMR data analysis. Run [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/SPSCAN SPSCAN] to conver Buffalo.NMRPipe format data to [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY] format data if use [http://www.nsm.buffalo.edu/Chem/HTP_twiki43/bin/view/NESG/XEASY XEASY].