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Agilent
Technologies
VnmrJ BioPack:
The Easiest Path to High Quality BioNMR Data
Evgeny Tishchenko Frank Delaglio
Agilent BioPack eSeminar
Santa Clara August 2013
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VnmrJ 4.0
2
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VnmrJ 4.0 and NMRPipe
3
The NMRPipe engine extends to Bio, Solids, and Small-molecule applications
TALOS+: protein backbone phi,psi torsions
from chemical shifts.
SPARTA+: protein backbone chemical
shifts from structure.
DYNAMO/PDBUTIL: structure analysis and
manipulation, add protons, create
extended structures, etc.
DC: manipulation of Dipolar Couplings,
NMR Homology Search (MFR).
IST: 2D and 3D NUS processing.
Spectral Alignment for CRAFT.
SpecView: 1D and 2D spectral series
analysis with Interactive Principal
Component Analysis Navigation.
SPARTA+
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TALOS+ predicts protein backbone torsions from chemical shifts using a
combination of database mining and an artificial neural network (ANN).
It can form predictions for 88% of residues on average, with an RMS of
better than 15 degrees. A No-Proton mode tuned for Solid State
applications is included.
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Page 5
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SPARTA+
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• Create Extended Structure
• Add Protons
• Transformations of PDB Coordinates
• List Secondary Structure, H-Bonds
• Mass, Volume, Surface Area
• Simple simulated annealing
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Analyze Titration Curve to Estimate Kd
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VnmrJ 4.0 – NMRPipe SpecView
10
1D Series Display with Interactive Principal Component Analysis
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VnmrJ 4.0 – NMRPipe SpecView
11
2D Series Display with Interactive Principal Component Analysis
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VnmrJ 4.0 BioPack and NMRPipe
12
NMRPipe – The Old Way
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VnmrJ 4.0 BioPack and NMRPipe
13
NMRPipe – The Old Way
Manually Select Acquisition Mode
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VnmrJ 4.0 BioPack and NMRPipe
14
NMRPipe – The Old Way
Manually Select Nucleus
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VnmrJ 4.0 BioPack and NMRPipe
15
NMRPipe – The Old Way
Manually Select Axis Label
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VnmrJ 4.0 BioPack and NMRPipe
16
NMRPipe – The Old Way
Traditionally, NMRPipe scripts are manually edited to set parameter values
#!/bin/csh
xyz2pipe -in fid/test%03d.fid -x -verb \
| nmrPipe -fn SOL \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5 \
| nmrPipe -fn ZF \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 43.0 -p1 0.0 -di \
| nmrPipe -fn EXT –x1 10.5ppm –xn 5.7ppm -sw \
| nmrPipe -fn TP \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0 \
| nmrPipe -fn ZF \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 -90.0 -p1 180.0 -di \
| nmrPipe -fn TP \
| nmrPipe -fn POLY -auto \
| pipe2xyz -out ft/test%03d.ft2 -x -to 0
xyz2pipe -in ft/test%03d.ft2 -z -verb \
| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF \
| nmrPipe -fn FT \
| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \
| pipe2xyz -out ft/test%03d.ft3 -z
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VnmrJ 4.0 BioPack and NMRPipe
17
BioPack and NMRPipe – Automated Construction of Processing Schemes
Automatically Create and Run
NMRPipe Scripts
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VnmrJ 4.0 BioPack and NMRPipe
18
BioPack and NMRPipe – Automated Construction of Processing Schemes
The VnmrJ “Do it All” Button
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VnmrJ 4.0 BioPack and BioPack Express
19
BioNMR Setup and Processing with Just a Few Clicks
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VnmrJ 4.0 and Non-Uniform Sampling
20
Background: the Fourier Transform and Non-Uniform Sampling
X( f ) = S x( t ) [ cos( 2pft / N ) - i sin( 2pft / N ) ]
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S+ S-
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S+ S-
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S+ S-
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Page 27
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Page 28
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Non-Uniform Sampling on a Uniform Grid
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Non-Uniform Sampling: Skip a Fraction of the Points
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Non-Uniform Sampling
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Non-Uniform Sampling:
for Fourier Transform, Replace Missing Points with Zeros
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S+ S-
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Linear versus Non Uniform Sampling
35
Linear Sampling: Broad Line and Periodic Truncation Wiggles
Non Uniform Sampling: Narrow Line and Random Noise-Like Artifacts
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Non Uniform Sampling
36
Threshold Methods
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Non Uniform Sampling
37
Threshold Methods
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Non Uniform Sampling
38
Threshold Methods
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Non Uniform Sampling
39
IST – Iterative Soft Thresholding
Fourier Spectrum IST Spectrum
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Page 40
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Non Uniform Sampling
41
Non-Uniform Sampling and NMRPipe in VnmrJ 4
Pulse sequence-independent data acquisition:
o Works seemlessly with every experiment, automatically.
o Effortless - just set check a NUS checkbox in the graphical interface.
o Comprehensive set of options for sampling schedules, including any
user-supplied schedule.
o NMRPipe Users - No need to figure out data acquisition order, reshuffling
dimensions etc… No hassle, just press the processing button.
o NUS Reconstruction is handled automatically – no need to download and
learn complicated signal processing software packages from academic
labs, no need to construct NMRPipe scripts by hand.
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BioPack Express – Introduced at ENC 2013
42
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BioPack Express
43
An overview
BioPack:
An comprehensive software framework for automated, optimized
bioNMR measurement setup, with fully-automated, supllemented
with the most extensive library of pulse sequences. BioPack
provides expert users with ultimate control over all experimental
parameters.
BioPack Express:
A streamlined enhancement to BioPack that allows a user to acquire
the most commonly used bioNMR experiments with near optimum
performance and minimum operator involvement.
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BioPack Express
44
BioPack Express fundamentals
A vast majority of bioNMR experiments require very few “input
parameters” in order to get decent results:
o What experiments to run (i.e. HNCA, HSQC , etc.)
o Spectrometer time available (i.e. nt, NUS or not)
o One or two “specials” per experiment (ex. mixing time in
TOCSY/NOESY, max T2 in CPMGs, etc.)
Everything else can be predicted based on knowledge about the nature
of a particular experiment and spectrometer calibrations
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BioPack Express
45
A single panel is sufficient to acquire, and process the most widely-used experiments
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BioPack Express
46
BioPackExpress Features
o Intuitive high-level user interface that allows a user to set up and run a
bioNMR experiment or a queued set of experiments with a few clicks of
a button.
o NUS made easy: automatic experiment-specific and pulse-sequence
independent set-up for Non-Uniform data acquisition and processing.
o Automatic set-up of data processing parameters.
o Top-level acquisition and processing algorithms are experiment-specific
and can be easily customized, while a unified graphical interface is used
for all experiment types.
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BioPack Express
47
In most cases one would need only one panel
Quick calibration of 1H pw90 (needed once per sample)
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BioPack Express
48
In most cases one would need only one panel
Key experiment parameters
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BioPack Express
49
In most cases one would need only one panel
Non-Uniform Sampling
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BioPack Express
50
In most cases one would need only one panel
Human-readable choices of experiment modes (experiment-specific!)
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BioPack Express
51
In most cases one would need only one panel
Human-readable options for data processing (dataset-specific!)
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BioPack Express
52
In most cases one would need only one panel
Hint/info line
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BioPack Express
53
How to setup a single experiment
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54
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BioPack Express
55
How to setup a queue of experiments
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BioPack Express
56
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BioPack Express
57
How to process
a multidimensional dataset
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BioPack Express
58
How to process
a multidimensional dataset
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BioPack Express
59
How to process
a multidimensional dataset
acquired using Non-Uniform Sampling
( NUS)
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BioPack Express
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Agilent VnmrJ BioPack Express
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The Most Widely-Used BioNMR Experiments in Just a Few Mouse Clicks
Shown here:
o NUS HNCO
o NUS HNCACB
o NUS HNCA
o NUS HC(CO)HN
o N15NOE
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Agilent Spinsights NMR Community
62
https://spinsights.chem.agilent.com
Note: registration is required to access the Spinsights online community.
More Questions?
Join the Spinsights NMR Community and
Help Yourself, Help Each Other, or Ask
Agilent
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Thank You!
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