REDCAT: Difference between revisions
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== '''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. | ||
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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. | ||
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== '''Features''' == | |||
== '''Features''' == | |||
The following lists some of the features of REDCAT: | The following lists some of the features of REDCAT: | ||
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*Dynamic averaging of RDCs due to motion | *Dynamic averaging of RDCs due to motion | ||
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== '''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> | ||
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Revision as of 17:41, 2 December 2009
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