REDCAT - Revision history

Jma at 20:53, 6 January 2010

2010-01-06T20:53:05Z

← Older revision		Revision as of 20:53, 6 January 2010
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Recent availability and utility of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data ~~(Ref.~~ 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.		Recent availability and utility of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data [1]. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.

	Conventional use of REDCAT requires existence of molecular structure and assigned RDC data. In the presence of structure and assigned data, REDCAT can be used to scrutinize the validity of a structure, study internal motion, orient rigid domains with respect to each other and emulate RDC data under static and dynamic conditions.		Conventional use of REDCAT requires existence of molecular structure and assigned RDC data. In the presence of structure and assigned data, REDCAT can be used to scrutinize the validity of a structure, study internal motion, orient rigid domains with respect to each other and emulate RDC data under static and dynamic conditions.
Line 9:		Line 9:
	More descriptive on-line documentation and tutorials on REDCAT can be found at the following [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat link].		More descriptive on-line documentation and tutorials on REDCAT can be found at the following [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat link].

	<br>		<br>

	== '''Features''' ==		== '''Features''' ==

Jma at 20:52, 6 January 2010

2010-01-06T20:52:43Z

← Older revision		Revision as of 20:52, 6 January 2010
Line 81:		Line 81:

	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>
			<br>
	<br>

	~~-- SonalBansal - Sept 2007~~

	~~-- HomayounValafar - Feb 2009~~

	~~-- Edited by JimAramini - Dec 2009~~

	<br>		<br>

Jma at 18:27, 2 December 2009

2009-12-02T18:27:46Z

← Older revision		Revision as of 18:27, 2 December 2009
Line 7:		Line 7:
	A number of improved algorithms have been incorporated to obtain order tensors and back calculate couplings from a given order tensor and proposed structure. These include the proper sampling of the Null-space (when the system of linear equations is underdetermined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging process.		A number of improved algorithms have been incorporated to obtain order tensors and back calculate couplings from a given order tensor and proposed structure. These include the proper sampling of the Null-space (when the system of linear equations is underdetermined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging process.

	More descriptive on-line documentation and tutorials on REDCAT can be found at the following [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat link].		More descriptive on-line documentation and tutorials on REDCAT can be found at the following [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat link].


			<br>

	== '''Features''' ==		== '''Features''' ==
Line 27:		Line 27:
	<br>		<br>

	== '''Downloading and Installing REDCAT''' ==		== '''Downloading and Installing REDCAT''' ==

	~~Instructions for downloading REDCAT and its installation can be found at this [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat:Installation link].~~

			Instructions for downloading REDCAT and its installation can be found at this [http://ifestos.cse.sc.edu/wiki/html/index.php/Redcat:Installation link].

			<br>

	== '''Finding the Alignment Tensor Using REDCAT''' ==		== '''Finding the Alignment Tensor Using REDCAT''' ==

	*Prepare your rdc data as a single column text file with a list of rdc scalar couplings in hz. The rdc couplings must be from a block of consequtive residues within you protein. You must know the starting residue and ending residue numbers for this block. For residues within the block that you do not know the couplings for, use 999 to indicate an unknown coupling.		*Prepare your rdc data as a single column text file with a list of rdc scalar couplings in hz. The rdc couplings must be from a block of consequtive residues within you protein. You must know the starting residue and ending residue numbers for this block. For residues within the block that you do not know the couplings for, use 999 to indicate an unknown coupling.
Line 40:		Line 40:
	*Go to the 'FILE' menu and select 'Prepare Input' the menu will look like that shown in Figure 1.<br>		*Go to the 'FILE' menu and select 'Prepare Input' the menu will look like that shown in Figure 1.<br>

	==== Figure 1: Image of "prepare input" menu from REDCAT ====		==== Figure 1: Image of "prepare input" menu from REDCAT ====

	[[Image:REDCATinputMenu.jpg]]		[[Image:REDCATinputMenu.jpg]]

	*Enter the name of your PDB file under 'PDB Input file'.		*Enter the name of your PDB file under 'PDB Input file'.
Line 64:		Line 64:
	*Write down the Sxx, Syy, and Szz values of the best solutions. These are relative to max rdc value. Multiply them by (for example 24350 for NH) to get the values to use for calculating Da and R.		*Write down the Sxx, Syy, and Szz values of the best solutions. These are relative to max rdc value. Multiply them by (for example 24350 for NH) to get the values to use for calculating Da and R.

			<br>

			== '''Finding the Q-Factor Using REDCAT''' ==
	~~=== <br> ===~~

	== '''Finding the Q-Factor Using REDCAT''' ==

	*You must first have loaded or build a redcat file from a pdb structure, populated it with rdc values, and found the alignment tensor and euler angles as described above.		*You must first have loaded or build a redcat file from a pdb structure, populated it with rdc values, and found the alignment tensor and euler angles as described above.
Line 78:		Line 76:
	*The rmsd between the measured and calculated rdcs and the Quality Factor will show up at the bottom of the window.		*The rmsd between the measured and calculated rdcs and the Quality Factor will show up at the bottom of the window.

			<br>

	== '''References''' ==		== '''References''' ==
Line 84:		Line 82:
	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>

			<br>

			-- SonalBansal - Sept 2007

	~~-- SonalBansal - Sept 2007~~		-- HomayounValafar - Feb 2009

	-- HomayounValafar - Feb 2009

	-- Edited by JimAramini - Dec 2009		-- Edited by JimAramini - Dec 2009

	<br>		<br>

Jma at 18:27, 2 December 2009

2009-12-02T18:27:03Z

@@ Line 1: / Line 1: @@
 == '''Introduction'''  ==
-Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data (Ref. 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.
+Recent availability and utility of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data (Ref. 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.
-Conventional use of REDCAT requires existence of molecular structure and assigned RDC data. In the presence of structure and assigned data, REDCAT can be used to scrutenize the validity of a structure, study internal motion, orient rigid domains with respect to each other and emulate RDC data under static and dynamic conditions.
+Conventional use of REDCAT requires existence of molecular structure and assigned RDC data. In the presence of structure and assigned data, REDCAT can be used to scrutinize the validity of a structure, study internal motion, orient rigid domains with respect to each other and emulate RDC data under static and dynamic conditions.
 == '''Features'''  ==
@@ Line 24: / Line 26: @@
 <br>
 == '''References'''  ==
 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>
 <br>

Jma at 17:41, 2 December 2009

2009-12-02T17:41:50Z

← Older revision		Revision as of 17:41, 2 December 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data (Ref. 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.		Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data (Ref. 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.
Line 7:		Line 7:
	obtain order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is underdetermined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging process.		obtain order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is underdetermined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging process.

			[[Image:Front.png]]<br>

			== '''Features''' ==
	== '''Features''' ==

	The following lists some of the features of REDCAT:		The following lists some of the features of REDCAT:
Line 23:		Line 23:
	*Dynamic averaging of RDCs due to motion		*Dynamic averaging of RDCs due to motion

			<br>

			== '''References''' ==

	== ~~'''References'''~~ ==		[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241] <br>

	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241]
	<br>		<br>
	~~== <span class="editsection">[[http://ifestos.cse.sc.edu/wiki/html/index.php?title=Redcat&action=edit&section=3 edit]]</span> ==~~

Jma: Created page with '== '''Introduction''' == Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual…'

2009-12-02T17:33:43Z

Created page with '== '''Introduction''' == Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual…'

New page

== '''Introduction''' ==

Recent availability of residual dipolar couplings (RDC) data has highlighted the need for general and user friendly RDC analysis tools. REDCAT (REsidual Dipolar Coupling Analysis Tool) has been designed and distributed as a general tool for analysis of RDC data (Ref. 1). REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk and is therefore highly portable. The computational engine behind this GUI is written in C/C++ providing excellent computational performance. Separation of the computational engine from the graphical engine allows for flexible and easy command line interaction that can used for automated data analysis sessions.

Conventional use of REDCAT requires existence of molecular structure and assigned RDC data. In the presence of structure and assigned data, REDCAT can be used to scrutenize the validity of a structure, study internal motion, orient rigid domains with respect to each other and emulate RDC data under static and dynamic conditions.

obtain order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is underdetermined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging process.

== '''Features''' ==

The following lists some of the features of REDCAT:

*Easy manipulation of the data during an analysis session via the GUI implementation
*Easy extraction of principal order parameters, GDO, Szz, eta and the Euler angles that allow the transformation of a structure into its principle alignment frame (PAF)
*More meaningful methods of screening for valid order tensor solutions
*Back-calculation of RDCs with any given tensor and structure
*Calculation of the rmsd and Q-factor between back calculated and measured RDCs
*Report of the best solution tensor (in the rmsd sense)
*Error analysis that allows the identification and isolation of problematic measurements or structural errors
*Computation of error values that will produce solutions for the given coordinates and RDC data
*Dynamic averaging of RDCs due to motion

== '''References''' ==

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJX-4BJWWY6-2&_user=521354&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000026038&_version=1&_urlVersion=0&_userid=521354&md5=978a5b8d1cf72110c78cc737e2e15195 1- Homayoun Valafar and James H. Prestegard, REDCAT: a residual dipolar coupling analysis tool, Journal of Magnetic Resonance, Volume 167, Issue 2, April 2004, Pages 228-241]
<br>
== <span class="editsection">[[http://ifestos.cse.sc.edu/wiki/html/index.php?title=Redcat&action=edit&section=3 edit]]</span> ==