(Click here
to see the list of new features included in the version 3.5)
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Translator that allows the user to input pulse sequences using the
programming language of an actual experiment and/or to execute the same
pulse programs used on actual spectrometers; the current version supports
Bruker programming language (versions 2.5 and earlier); this module
is written in Lex and Matlab, It is intended (P. 1, Table below) to make
it very general and extensible (e.g. include Varian pulse sequences).
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Graphical User Interface that resembles an actual spectrometer interface
(Click here
to see it).
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Spin System Setup module includes both text and graphical modes and
relaxation-rate calculator to help the user define a desired spin system. We
have started creating a library (P. 2) of
typical spin systems (e.g. AMX, A3X, A3B2, some
typical chemical compounds s including amino acids ) to be
directly loaded from disk, to ease creation of the spin system.
This will be part (P. 3) of creating an optional simple interface for teaching
purposes.
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Simulator that executes the translated program code and produces
an "experimental" data set. Currently allows simulation of single- and
multichannel 1D, 2D, and 3D NMR experiments including rectangular and shaped
RF pulses and pulsed field gradients. Other features include spin decoupling,
power level selection and switching during experiment, direct or indirect
detection of heteronuclei, and automatic or manual selection of fine steps
for calculation of spin density evolution.
Current version supports spin-1/2 nuclei (e.g. 1H, 15N,
and 13C), the actual number of spins is limited only by the
size of addressable memory. The user can add/simulate the effect of experimental
noise. Suggested future modification include
(P. 4) specific implementation of complex decoupling schemes and other arbitrary
phase/amplitude/offset pulse trains. In addition, we plan (P. 7)
to incorporate specifically chemical exchange.
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Pulsed Field Gradients: this version includes two different computational
approaches, which permit efficient treatment of experiments using pulsed
field gradients for coherence selection:
-- an explicit calculation of all coherence transfer pathways (CTP)
in an experiment, and
-- a multi-layer ('Salami') approach.
Future modifications
will include (P. 6) transverse gradients.
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Data Processing module that allows all typical spectrum processing
features (such as apodization, zero-filling, linear phase correction, and
phase sensitive detection by TPPI, States, States-TPPI, and echo-antiecho
methods). A future modification (P. 8) will extend processing to arbitrary
multiple dimensions and (P. 9) multiple acquisitions per pulse train.
Once the data structure is defined properly, these features will
be added into the simulator driver, the GUI setup, and the translator.
The addition of other standard processing features like (P. 14) Linear prediction
are also possible.
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Visualization Modules that trace and display the spin density, expressed
as a linear combination of basis operators, as it evolves during an experiment.
A future modification (P. 10) would be the visualization of coherence
order during the sequence, which will require modifications to the simulator.
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Interfaces to other software available in the current version allow the
user to export simulated data in XWINNMR and NMRPipe formats and to import
experimental data (from Bruker) in order to analyze them using the tools
available in the Virtual Spectrometer package.
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In the future, additions are expected to involve (P. 11) extending the
Hamiltonian used in the simulator to solids-specific features;
(P. 12) extension to account for diffusion in PFGs; (P. 13) extensions, in
a new module, to account for instrumental issues (filters, effects of digitization,
RF inhomogeneties, Q instabilities)
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