AutoStructure - Revision history

Jma at 21:25, 6 January 2010

2010-01-06T21:25:27Z

← Older revision		Revision as of 21:25, 6 January 2010
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	AutoStructure is a protein structure determination tool that uses uninterpreted NOESY cross peaks together with structure calculation programs like XPLOR or DYANA to generate a 3D structure of the protein that is as close to the true structure as possible ~~(Ref.~~ 1). AutoStructure uses an iterative bottom-up topology-constrained approach to analyze NOE peak lists. It first builds an initial fold based on intraresidue and sequential NOESY data, together with characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unique long-range packing NOE interactions based on chemical shift matching and symmetry considerations. Unassigned NOESY cross peaks are not used in structure calculations. Additional NOESY cross peaks are iteratively assigned using intermediate structures and the knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. This protocol, in principal, resembles the methodology that an expert would utilize in manually solving a protein structure by NMR.		AutoStructure is a protein structure determination tool that uses uninterpreted NOESY cross peaks together with structure calculation programs like XPLOR or DYANA to generate a 3D structure of the protein that is as close to the true structure as possible [1]. AutoStructure uses an iterative bottom-up topology-constrained approach to analyze NOE peak lists. It first builds an initial fold based on intraresidue and sequential NOESY data, together with characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unique long-range packing NOE interactions based on chemical shift matching and symmetry considerations. Unassigned NOESY cross peaks are not used in structure calculations. Additional NOESY cross peaks are iteratively assigned using intermediate structures and the knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. This protocol, in principal, resembles the methodology that an expert would utilize in manually solving a protein structure by NMR.

	The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores ~~(Ref.~~ 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.		The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores [2]. Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

	The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.
Line 141:		Line 141:
	== '''References''' ==		== '''References''' ==

	1.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		[http://www.ncbi.nlm.nih.gov/pubmed/16374783?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1 1.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.]

	2.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.		[http://www.ncbi.nlm.nih.gov/pubmed/15701001?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.]

	<br>		<br>
Line 149:		Line 149:
	<br>		<br>

	<br>		<br>

	~~<br>~~

	~~-- JimAramini - 07 Nov 2009~~

Yphuang at 21:05, 18 December 2009

2009-12-18T21:05:39Z

← Older revision		Revision as of 21:05, 18 December 2009
Line 9:		Line 9:
	As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the program is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options as well as [[Structure Calculation Using AS-DP\|AS-DP]].  Please contact [mailto:yphuang@cabm.rutgers.edu Janet Huang] for further information on future releases.<br>		As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the program is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options as well as [[Structure Calculation Using AS-DP\|AS-DP]].  Please contact [mailto:yphuang@cabm.rutgers.edu Janet Huang] for further information on future releases.<br>



	== '''Getting Started''' ==		== '''Getting Started''' ==
Line 75:		Line 75:
	==== Figure 1:  AutoStructure main page ====		==== Figure 1:  AutoStructure main page ====

	[[Image:AS mainpage.png]]		[[Image:AS mainpage.png\|466x365px]]

	=== Control File<br> ===		=== Control File<br> ===
Line 87:		Line 87:
	==== Figure 2: AutoStructure control file: General Section ====		==== Figure 2: AutoStructure control file: General Section ====

	[[Image:AScontrolfile general.png]]		[[Image:AScontrolfile general.png\|505x536px]]

	*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.		*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.
Line 94:		Line 94:
	==== Figure 3: AutoStructure control file: PeakList Section ====		==== Figure 3: AutoStructure control file: PeakList Section ====

	[[Image:AScontrolfile peaks.png]]		[[Image:AScontrolfile peaks.png\|534x549px]]

	<br>		<br>
Line 106:		Line 106:
	*Under the Autostructure pull-down on the main page, choosing Start -> Calc opens the dialogue box below.		*Under the Autostructure pull-down on the main page, choosing Start -> Calc opens the dialogue box below.

	[[Image:AS startCalc.png]]		[[Image:AS startCalc.png\|515x573px]]

	*Launching calculations from the GUI uses is generally slow since only the processors on your own machine are used.  To speed up the calculations use the command line on a cluster.		*Launching calculations from the GUI uses is generally slow since only the processors on your own machine are used.  To speed up the calculations use the command line on a cluster.

Jma at 22:49, 10 November 2009

2009-11-10T22:49:49Z

← Older revision		Revision as of 22:49, 10 November 2009
Line 5:		Line 5:
	The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.		The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

	The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

	As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the ~~prgram~~ is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options as well as [[~~Structure_Calculation_Using_AS~~-DP\|AS-DP]].<br>		As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the program is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options as well as [[Structure Calculation Using AS-DP\|AS-DP]].  Please contact [mailto:yphuang@cabm.rutgers.edu Janet Huang] for further information on future releases.<br>

Jma at 01:52, 10 November 2009

2009-11-10T01:52:42Z

← Older revision		Revision as of 01:52, 10 November 2009
Line 7:		Line 7:
	The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

	As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the prgram is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options.<br>		As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the prgram is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options as well as [[Structure_Calculation_Using_AS-DP\|AS-DP]].<br>



	== '''Getting Started''' ==		== '''Getting Started''' ==

Jma at 01:43, 10 November 2009

2009-11-10T01:43:12Z

← Older revision		Revision as of 01:43, 10 November 2009
Line 7:		Line 7:
	The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

	As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the prgram is 2.2.1.		As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the prgram is 2.2.1.  This version does not support structure calculations on dimers or including RDC's; a new version of the program is in development, and will support these options.<br>

	== '''Getting Started''' ==		== '''Getting Started''' ==

Jma at 17:01, 9 November 2009

2009-11-09T17:01:15Z

← Older revision		Revision as of 17:01, 9 November 2009
Line 5:		Line 5:
	The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.		The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

	~~ ~~The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

			As of Nov. 2009, the latest [[Media:AutoManual_2.1.1.pdf\|manual]] for AutoStructure covers version 2.1.1; the current version of the prgram is 2.2.1.

	== '''Getting Started''' ==		== '''Getting Started''' ==

Jma at 04:41, 8 November 2009

2009-11-08T04:41:03Z

← Older revision		Revision as of 04:41, 8 November 2009
Line 5:		Line 5:
	The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.		The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

	The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.		The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

	== '''Getting Started''' ==		== '''Getting Started''' ==
Line 81:		Line 81:
	*General:  general input files for the AutoStructure run (Figure 2).<br>		*General:  general input files for the AutoStructure run (Figure 2).<br>

	==== Figure 2: AutoStructure control file: General Section ====		==== Figure 2: AutoStructure control file: General Section ====

	[[Image:AScontrolfile general.png]]		[[Image:AScontrolfile general.png]]

	*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.		*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.
	*Peak Lists:  peak lists for the AutoStructure run (Figure 3).		*Peak Lists:  peak lists for the AutoStructure run (Figure 3). Note that AutoStructure can take into account aliasing in any dimension; simply enter the sweep width of the aliased dimesnion(s).  Also, we generally combine aliphatic and aromatic <sup>13</sup>C-edited NOESY peak lists into a single list for an AutoStructure run.<br>

	==== Figure 3: AutoStructure control file: PeakList Section ====		==== Figure 3: AutoStructure control file: PeakList Section ====

	[[Image:AScontrolfile peaks.png]]		[[Image:AScontrolfile peaks.png]]
Line 137:		Line 137:
	== '''References''' ==		== '''References''' ==

	1.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		1.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

	2.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.		2.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.
Line 147:		Line 147:
	<br>		<br>

			<br>

	-- JimAramini - 07 Nov 2009		-- JimAramini - 07 Nov 2009

Jma at 21:46, 7 November 2009

2009-11-07T21:46:29Z

← Older revision		Revision as of 21:46, 7 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

			AutoStructure is a protein structure determination tool that uses uninterpreted NOESY cross peaks together with structure calculation programs like XPLOR or DYANA to generate a 3D structure of the protein that is as close to the true structure as possible (Ref. 1). AutoStructure uses an iterative bottom-up topology-constrained approach to analyze NOE peak lists. It first builds an initial fold based on intraresidue and sequential NOESY data, together with characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unique long-range packing NOE interactions based on chemical shift matching and symmetry considerations. Unassigned NOESY cross peaks are not used in structure calculations. Additional NOESY cross peaks are iteratively assigned using intermediate structures and the knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. This protocol, in principal, resembles the methodology that an expert would utilize in manually solving a protein structure by NMR.

			The RPF program within AutoStructure uses a novel, rapid, and simple approach for calculating global structure quality scores (Ref. 2). Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

			The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 3D and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

	== '''Getting Started''' ==		== '''Getting Started''' ==
Line 65:		Line 71:
	==== Figure 1:  AutoStructure main page ====		==== Figure 1:  AutoStructure main page ====

	[[Image:~~AS_mainpage~~.png]]		[[Image:AS mainpage.png]]

	=== Control File<br> ===		=== Control File<br> ===

	The control file is the central file which defines the input, parameter, and execution files and options for an AutoStructure run.		The control file is the central file which defines the input, parameter, and execution files and options for an AutoStructure run.

			It is easiest to manipulate the control file using the GUI.  The control file in the GUI is subdivided into three main sections:

	~~It is easiest to manipulate the control file using the GUI.~~  ~~The control file in~~ the ~~GUI is subdivided into three main sections:~~		*General:  general input files for the AutoStructure run (Figure 2).<br>

	*General:~~  general input files for the~~ AutoStructure ~~run.~~		==== Figure 2: AutoStructure control file: General Section ====

	[[Image:~~AScontrolfile_general~~.png]]		[[Image:AScontrolfile general.png]]

	*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.		*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.
	*Peak Lists:  peak lists for the AutoStructure run.		*Peak Lists:  peak lists for the AutoStructure run (Figure 3).

	~~[[Image~~:~~AScontrolfile_peaks.png]]~~		==== Figure 3: AutoStructure control file: PeakList Section ====

			[[Image:AScontrolfile peaks.png]]

			<br>

	=== Starting a Calculation ===		=== Starting a Calculation ===
Line 126:		Line 136:
	</pre>		</pre>
	== '''References''' ==		== '''References''' ==

			1.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

			2.    Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.''J. Am. Chem. Soc. 127'', 1665-1674.

			<br>

			<br>

			<br>



	-- JimAramini - 07 Nov 2009		-- JimAramini - 07 Nov 2009

Jma at 21:31, 7 November 2009

2009-11-07T21:31:14Z

← Older revision		Revision as of 21:31, 7 November 2009
Line 46:		Line 46:
	Other files that can be included in an AutoStructure calculation inlcude:		Other files that can be included in an AutoStructure calculation inlcude:

	*<sup>H</sup>N-H<sup>α</sup> J-couplings:  used for initial secondary ~~structrue~~ anlysis		*<sup>H</sup>N-H<sup>α</sup> J-couplings:  used for initial secondary structure anlysis
	*slow exchanging NH list:  used for initial secondary structrue anlysis		*slow exchanging NH list:  used for initial secondary structrue anlysis
	*dihedral angle constraints:  used directly in CYANA/XPLOR structure calculations		*dihedral angle constraints:  used directly in CYANA/XPLOR structure calculations
Line 64:		Line 64:

	==== Figure 1:  AutoStructure main page ====		==== Figure 1:  AutoStructure main page ====

			[[Image:AS_mainpage.png]]

	=== Control File<br> ===		=== Control File<br> ===

			The control file is the central file which defines the input, parameter, and execution files and options for an AutoStructure run.

			It is easiest to manipulate the control file using the GUI.  The control file in the GUI is subdivided into three main sections:

			*General:  general input files for the AutoStructure run.

			[[Image:AScontrolfile_general.png]]

			*Command:  specific command input and selections for the AutoStructure run.  This will be discussed in another section.
			*Peak Lists:  peak lists for the AutoStructure run.

			[[Image:AScontrolfile_peaks.png]]



	=== Starting a Calculation ===		=== Starting a Calculation ===

Jma at 21:12, 7 November 2009

2009-11-07T21:12:41Z

← Older revision		Revision as of 21:12, 7 November 2009
Line 44:		Line 44:
	==== Other input files ====		==== Other input files ====

	Other files that can be included in an AutoStructure calculation inlcude:		Other files that can be included in an AutoStructure calculation inlcude:

	*<sup>H</sup>N-H<sup>α</sup> J-couplings:  used for initial secondary structrue anlysis		*<sup>H</sup>N-H<sup>α</sup> J-couplings:  used for initial secondary structrue anlysis
	*slow exchanging NH list:  used for initial secondary structrue anlysis		*slow exchanging NH list:  used for initial secondary structrue anlysis
	*dihedral angle constraints:  used directly in CYANA/XPLOR structure calculations		*dihedral angle constraints:  used directly in CYANA/XPLOR structure calculations
	*maunal distance constraints:  used directly in CYANA/XPLOR structure calculations		*maunal distance constraints:  used directly in CYANA/XPLOR structure calculations

	=== Graphical User Interface ===		=== Graphical User Interface ===

	AutoStructure features a GUI which is particularly useful for preparing the control file for and subsequent analysis of structure calulations.		AutoStructure features a GUI which is particularly useful for preparing the control file for and subsequent analysis of structure calulations.

	The main page (Figure 1) features the following pull-down menus:		The main page (Figure 1) features the following pull-down menus:

	*File:  manipulation of control file		*File:  manipulation of control file
	*AutoStructure:  starting an AutoStructure run and analysis of an output directory		*AutoStructure:  starting an AutoStructure run and analysis of an output directory
	*AutoQF(RPF):  starting an RPF analysis and analysis of an RPF directory		*AutoQF(RPF):  starting an RPF analysis and analysis of an RPF directory
	*PDB Tools:  tools for converting PDB coordinates to IUPAC format		*PDB Tools:  tools for converting PDB coordinates to IUPAC format
	*Misc Tools		*Misc Tools

	==== Figure 1:  AutoStructure main page ====		==== Figure 1:  AutoStructure main page ====



	=== Control File<br> ===		=== Control File<br> ===

	=== ~~Staring~~ a Calculation ===		=== Starting a Calculation ===

	The user can start a calculation from either the graphical user face or the command line.		The user can start a calculation from either the graphical user face or the command line.
Line 109:		Line 107:
	-v Calculate the M score and average shifts		-v Calculate the M score and average shifts

	</pre>		</pre>
	~~== '''Files for Download''' ==~~

	== '''References''' ==		== '''References''' ==

	-- JimAramini - 07 Nov 2009		-- JimAramini - 07 Nov 2009