Extended Histogram Method (EHM) for analysis of
correlated residual dipolar couplings
Grid search procedure for limited sets of correlated residual dipolar
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
(C) Corel Quattro Pro spreadsheet,
EHM.qpw, and instructions.
(D) MS Excel spreadsheet, EHM.xls,
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
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.
Thanks to Frank Delaglio for comments and assistance.
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Last updated: March 29, 2004.