NAME
nmrWish - Tcl/Tk Window Shell for Spectral Analysis
DESCRIPTION
The nmrWish program is a version of the Tcl/Tk window shell
wish, customized to include facilities for manipulation,
display, and analysis of multidimensional spectra and
images. It is a companion to the NMRPipe System, the spec-
tral processing system based on UNIX pipes (Delaglio et al.,
1995).
Tcl/Tk is a powerful and widely used command language which
includes facilities for graphical interface creation and for
communication between different applications; it was intro-
duced to the NMR community in the package NMRView (Johnson
and Blevins, 1994). The originator of Tcl/Tk, John
Ousterhaut, developed it initially to provide an extensible
command language for engineering applications (Ousterhaut,
1994).
A key feature of Tcl/Tk is the ability to construct a com-
plete graphical user interface as a simple script, rather
than as a lengthy compiled program. Because of its power
and convenience, Tcl/Tk has found use in thousands of scien-
tific and commercial applications, including those of NMR
spectrometer manufacturers and molecular modeling software
companies.
As a scripting language, Tcl includes facilities for manipu-
lating variables, text patterns, and lists, and for evaluat-
ing numerical expressions. It also provides basic text file
input/output, looping and conditional statements, and for
the definition of procedures. A special feature of Tcl is
the associative array, an array whose index is an arbitrary
text string rather than an integer, and whose contents may
be a combination of numeric or text data.
As a graphical interface language, Tk includes facilities
for creating various types of buttons and menus, as well as
items such as scrollbars and text editing windows. It also
includes facilities for rendering simple graphical items
such as polygons, ovals, and text. All of the graphical
items support many modes of interaction, so that interfaces
with options such as real-time drag-and-drop can be created.
In addition to the usual features of Tcl/Tk, the special
facilities of NMRWish include the following:
Region Extraction: Extraction or projection of arbitrary
spectral Regions of Interest (ROIs). Extracted regions
can be centered or aligned automatically through
interpolation, so that the extracted data corresponds to
the requested chemical shift coordinates regardless of
the digitization of the data. Furthermore, extracted
regions which exceed the measured chemical shift window
are unfolded and sign-adjusted automatically, so that
regions from related spectra can be manipulated or
displayed consistently even if they have differing spec-
tral windows.
Graphics of Spectra and Images: PostScript output with
completely customizable page layout is provided. Hard
copy of 1D spectra and 2D contours are available, as well
as hard copy modes for single images, three-image RGB
composites, and image vs. image scatter plots. More
recently, facilities for screen-based multi-window spec-
tral and image graphics have also been included.
Peak Detection: automated peak detection in 1D-4D,
including options for identifying peaks due to random
noise and truncation artifacts.
Relational Database Engine: a simple, general purpose
database engine, capable of manipulating peak tables,
assignments, and PDB format molecular coordinates.
Binary Manipulation: general facilities for reading,
writing, and manipulating binary data, including type
conversion (e.g. integer to float) general-purpose vector
processing commands and access to NMRPipe processing
functions. Specific commands for manipulating and inter-
preting NMRPipe-format data headers are also included.
Illustrations of nmrWish applications include spectral for-
mat conversion, custom hard-copy format design, peak picking
and peak evolution extraction, multi-spectrum visualization
and triple-resonance backbone assignment, automated genera-
tion of NOE constraints, and tools for SAR by NMR (Fessik et
al., 1996).
LEGAL NOTICES
The nmrWish program and its related software is based on a
design originating in the NIH Laboratory of Chemical Phy-
sics, NIDDK. It is not to be distributed or modified. (C)
F. Delaglio 1997.
The nmrWish program and its related software is provided
"as is". The NIH, the Laboratory of Chemical Physics,
NIDDK, and the authors make no warranties, either express
or implied, as to any matter whatsoever with respect
to the software. In particular, any and all warranties
of merchantability and fitness for any particular purpose
are expressly excluded. In no event will the NIH, the
Laboratory of Chemical Physics, NIDDK, or the authors be
liable for any loss of profits, any incidental, special,
exemplary, or consequential damages of any nature whatso-
ever (including without limitation, loss of use or other
commercial or research loss) arising out of or relating
to the use or performance of the software.
The nmrWish program makes use of GIF format images. The
Graphics Interchange Format(c) is the Copyright property of
CompuServe Incorporated. GIF(sm) is a Service Mark property
of CompuServe Incorporated.
For further information, please contact:
CompuServe Incorporated
Graphics Technology Department
5000 Arlington Center Boulevard
Columbus, Ohio 43220
USA
REFERENCES
Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer,
J., and Bax, A. (1995) J. Biomol. NMR, 6, 277-293.
Johnson, B. and Blevins, R.A. (1994) J. Biomol. NMR, 6,
277-293.
Ousterhout, J.K. (1994) Tcl and the Tk Toolkit, Addison-
Wesley, Reading MA.
Shuker, S.B., Hajduk, P.J., Meadows, R.P., and Fesik, S.W.
(1996) Science, 274, 1531-1534.