Extended Histogram Method (EHM) for analysis of correlated residual dipolar couplings
and
Grid search procedure for limited sets of correlated residual dipolar couplings


As described in the paper:

Application of Correlated Residual Dipolar Couplings to the Determination of the Molecular Alignment Tensor Magnitude of Oriented Proteins and Nucleic Acids, David L. Bryce and Ad Bax, J. Biomol. NMR 28: 273-278, 2004.

Downloads: You can download everything which is available here.  This tar file includes all four implementations of EHM as described in points 1(A) through 1(D), as well as the grid search method described in point 2, below.


1. Extended histogram method (EHM).
Options: (A) tcl script; or (B) QBasic program; or (C) Quattro Pro spreadsheet; or (D) MS Excel spreadsheet.

(A) New! Added March 29, 2004: A tcl script, ehm.tcl, and instructions.  Also includes ehm.com, which displays the results in a histogram using Frank Delaglio's showDC.tcl script.  Sample input and output files are provided.

Brief description:  Runs in the nmrWish/nmrPipe environment and takes as input a table of residual dipolar couplings, dObsA.tab, and produces as output: (i) a file in nmrPipe/Dynamo format, dEHMA.tab, which contains the original experimental data as well as the new synthetic dipolar couplings; (ii) a file, EHMsummary.txt, which provides values of Da and R on the basis of the standard histogram method as well as the extended histogram method.  Currently set up only for triplets of  1DNH, 1DCC', and 1DNC' RDCs in proteins.


(B) QBasic program, EHM.bas, and instructions.  Sample input and output files are included.

Brief description: The program runs on a PC under QBASIC (qbasic.exe or equivalent is required), and takes as input a text file containing an arbitrary number of sets of three RDCs, e.g.,1DNH, 1DCC', 1DNC', and produces as output: (i) a file “summary.txt” which contains a summary of the results, including the value of Da and R based on the extreme coupling values; (ii) a file “out.txt” which contains all the generated couplings (one degree increments within the plane, plus the couplings perpendicular to the planes); (iii) a file “out.dat” in CSOLIDS spectrum format, which may be used as input in WSOLIDS1 for simulating the powder pattern.  The relative angles at which the bond vectors lie may also be specified.  Equally applicable to protein and nucleic acid RDCs.  Currently the most flexible EHM implementation.

(C) Corel Quattro Pro spreadsheet, EHM.qpw, and instructions.

(D) MS Excel spreadsheet, EHM.xls, and instructions.

Brief description: Spreadsheets require as input sets consisting of three RDCs, e.g., 1DNH, 1DCC', 1DNC' in proteins and peptides, and provides all values of the couplings within the plane (at one degree increments) and the couplings perpendicular to the planes.  The relative angles at which the bond vectors lie may also be specified.  Equally applicable to protein and nucleic acid RDCs.


2. Grid search procedure for correlated RDCs.

(A) Scripts for systems on which nmrWish/nmrPipe are already installed.  Includes instructions, sample input data, and sample output.

Brief description: Grid search program in the tcl scripting language, which makes use of the “DC” program and existing modules of the NMRPipe software package, courtesy of Frank Delaglio (Delaglio et al., J. Biomol. NMR 6, 277-293 (1995)).  A postscript file displaying the chi2 contour plots is generated as output.  Equally applicable to protein and nucleic acid RDCs. The data format used is explained clearly here courtesy of Markus Zweckstetter.


Contact:   dbryce@speck.niddk.nih.gov
Thanks to Frank Delaglio for comments and assistance.

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Last updated: March 29, 2004.