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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Default BLOG Index

BLOG Index



University of Ottawa NMR Facility BLOG INDEX
March 2015


11B COSY
17O NMR of liquids
H20 vs D2O
1D selective HOESY
1H-19F
1H-31P
1D selective NOESY measurements
for exchanging roramers
1D TOCSY measurements
as a function of mixing time
for mixture analysis
1H NMR with X nucleus decoupling
1H[11B]
1H[13C]
1H[19F]
1H[27Al]
1H[31P]
2D correlation spectroscopy (COSY)
11B COSY
COSY 90 vs COSY 45
double quantum filtered
ECOSY for measurement of coupling constants
magnitude vs phase sensitive
vs TOCSY
2D exchange spectroscopy (EXSY)
and NOE (1)
and NOE (2)
2D heteronuclear Overhauser measurement (HOESY)
2D NMR
better data – more scans or more slices?
data apodization
phasing (video tutorial)
2D NOESY measurements
19F NOESY
and exchange (1)
and exchange (2)
choice of mixing time
effect of viscosity
phasing
phasing (video tutorial)
small vs large molecules
2D ROESY measurements
2D total correlation spectroscopy (TOCSY)
HSQC - TOCSY
TOCSY vs COSY
2H decoupling
2H NMR of liquids
chemical shift referencing in
on Bruker AVANCE spectrometers
Acoustic Ringing
backward linear prediction to correct for
pulse sequence to minimize
ASCII file generation
in TOPSPIN (1)
in TOPSPIN (2)
B1 Homogeneity
Background signals
11B
23Na
from dirty NMR probe
Background suppression
11B in liquids
11B in solids
Baseline correction
improving
in 2D NMR spectra
in solids MAS spectra of quadrupolar nuclides
Benchtop NMR
(1)
(2)
BIRD filter
Bloch decay vs Cross polarization
Chemical equivalence
Chemical exchange agents for spectral simplification
D2O shake
trifluorocaetic acid
Chemical shift referencing
1H in aqueous solution
external
in 2H NMR
Chemical shift tensors
and MAS sideband manifolds (1)
and MAS sideband manifolds (2)
effect of sample grinding on the measurement of
from static CP spectra
measurement from static solids spectra
Chemical shifts
concentration dependent
solvent effects – improving chemical shift resolution
temperature dependent
Concentration gradients
effect on spectral quality (1)
effect on spectral quality (2)
Coupling
13C – 14N
13C-14N-31P
13C – 19F
13C – 2H (1)
13C - 2H (2)
13C – 2H (3)
13C - 59Co
coupling between magnetically equivalent nuclei
signs of coupling constants vis ECOSY
virtual
Cross polarization for solid and CPMAS
CPMAS of household dust
effect of contact time
effect of MAS spinning speed
effect of quadrupolar nuclides on spin I = ˝ nuclides (1)
effect of quadrupolar nuclides on spin I = ˝ nuclides (2)
field dependence of chemical shift resolution in
importance of Hartman-Hahn match
in relation to MAS and high power decoupling
measurement of 13C 90 degree pulses with
measurement of relaxation times with
optimizing 1H decoupling in
ramped contact pulses
sensitivity improvement from
to distinguish solid polymorphs
vs Bloch decay
with FSLG HETCOR
Cross polarization with dipolar dephasing for solids
as an assignment tool
effect of spinning speed
with long dephasing delays (1)
with long dephasing delays (2)
Decoupler pulse calibration
in liquids
in solids
Decoupling
1H and 31P decoupling
1H decoupling and 13C signal-to-noise ratio
1H decoupling and 31P signal-to-noise ratio
11B decoupling
13C decoupling
19F decoupling
2H decoupling
27Al decoupling
31P decoupling
high power 1H decoupling in solids
homonuclear decoupling
modes of heteronuclear decoupling in liquids
DEPT
and quaternary alkyne carbon sites
APT vs DEPT 135
effect of 1H tuning on
missing signals in
of “acetone-d6”
of “perdeuterated “ solvents
vs DEPTQ
with 29Si
DEPTQ
vs DEPT
Diffusion and DOSY
diffusion in CPMG measurements
DOSY
Digital Filtering
Double presaturation
Dummy scans
Dynamic nuclear polarization (DNP)
Dynamic processes studied by 1D NMR
exchange studied by saturation transfer
exchanging rotamers
the NMR time scale
Earth’s field NMR
Echoes
CPMG
Fourier transform of
gradient spin echoes and selective excitation
simple spin echo
to remove 11B background in solids
Exponential line broadening
tutorial video
EZ NMR
tutorial video
Floor vibrations
effect on NMR spectra
Food and drink
candy cane
coffee
fruit cake
popcorn
rum and eggnog
shortbread cookies
Free induction decay
effects of truncation
Frequency shifted Lee-Goldberg CP-HETCOR for solids (CP-FSLG HETCOR)
Heat dissipation in Bruker spectrometers
Heteronuclear double quantum filter
HMBC experiments
HMQC responses in HMBC spectra
measuring 19F – 13C coupling in 1H - 13C HMBC
missing signals in
Nyquist fold-backs in
HMQC, HSQC and edited HSQC experiments
1H – 11B
19F – 13C
31P -109Ag
31P – 13C
doubled signals / poor decoupling
HMQC vs HSQC
HSQC - TOCSY
HSQC vs edited HSQC
isotope effects in 19F – 13C HMQC
multiple bond or weak one-bond correlations in
removing t1 noise in
Homonuclear 1H decoupling
Bloch-Siegert shifts
broadband 1H decoupled 1H spectra
HSQC-TOCSY
iPad / iPhone apps
Bruker Almanac
educational
Stanford University course on Fourier transforms vis iTunes U
Isotope effects
acetone
chloroform
complexed solvents
ethane
in 19F – 13C HMQC
methylene chloride
“perdeuterated” solvents
triphenyl phosphate
water
Kinetic measurements
Lineshape specification
erroneous
Linear prediction
backward
backward LP to correct for receiver overload
forward
forward LP for 2D data
Liquid crystalline samples
Lock
consequence of locking on the wrong solvent
how high should the lock signal be?
paramagnetic samples
spectra acquired with a sweeping field
spectral distortion from weak lock signal
Varian
Magic angle spinning for solids (MAS)
1H MAS
and available rf field
effect on Hartman-Hahn match
field dependence of chemical shift resolution
how fast to spin
how much sample
increasing signal-to-noise ration in
setting the magic angle (1)
setting the magic angle (2)
solution vs MAS spectra
rotor crashes
Magnet
accessing a used magnet
measurement of field drift
quench
Magnet cryogen fills and spectral quality
helium fills
helium one-way valve oscillation
nitrogen fills
nitrogen pressure in the magnet
Magnetic equivalence
Magnetic resonance imaging (MRI)
gradient calibration / 1D MRI
MRI photocopier
Nyquist fold-backs in MRI images
slice selection
why MRI scanners are loud
Measurement of long range C-H coupling constants
NMR acronyms
NMR of more than one isotope
23Na and 51V
NMR spectra without pulses
NMR spectrum frequency scale
NMR spectrum of dust (13C CPMAS)
NMR spectrum of hand cream (1H and 13C)
NMR spectrum of natural gas (1H)
NMR spectrum of TMS (1H)
NMR time scale
NMR tube thickness
NOE’s and decoupling
negative NOE’s and decoupling
positive NOE’s and decoupling
Nyquist fold-backs
and digital filtering
and mode of data acquisition
in HMBC data
in MRI
used to enhance satellite transitions in quadrupolar nuclides
Paramagnetism
13C spectra of paramagnetic compounds
determination of paramagnetic susceptibility
establishing the 2H lock for paramagnetic samples
paramagnetic shifts
the effect of paramagnetic oxygen
Phase of an NMR spectrum
first order phase errors
phasing a 1D spectrum (video tutorial)
phasing a 2D spectrum (video tutorial)
Probes
broadband vs inverse broadband
coil geometry
solids
why so expensive
Probe arcing
Probe tuning and matching
effect of 1H tuning on 13C spectra
effect of cable length
effect of sample spinning
effect on 90 degree pulse
probe electronics
problems with salty samples
Pulse calibration
effect of probe tuning
fast determination
for shaped pulses
for spin I = n/2 quadrupolar nuclei in solids
measurement of 13C pulses using cross polarization in solids
Pulse power measurements
expressed in dB Bruker vs Varian
expressed in Hz
pulses
Pulsed field gradients
calibration
dephasing ability
gradient spin echoes
recovery times
Purge pulses
QCPMG measurements
distortions in QCPMG spectra
for solid state 2H NMR
Quadrature detection
Quadrature images
Quadrature spikes
how to remove
Quantitative 1H NMR
Quantitative 13C NMR
finding lost 13C signals
Radiation damping
Receiver gain
and signal-to-noise ratio
backward LP to correct for receiver saturation
distortion from mis-setting
Relaxation
effect of paramagnetic oxygen
faster relaxation time measurements in solids
relaxation differences used to resolve overlapping signals
T1 anisotropy in solids
T1 measurement
T1r
T2 CPMG filter to enhance sharp lines
T2 measurements and diffusion
T2 vs T2*
Residual 1H signals for benzene-d6 and chloroform-d
Resolution enhancement
by using benzene as a solvent
Retrieving empty spinners from NMR magnets
Sample limitation
making the best of
Saturation transfer measurements
Scans
and signal-to-noise ratio
Shaped pulses and selective excitation or broadband inversion
broadband 180 degree pulses
calibration
excitation profiles (1)
excitation profiles (2)
for selective excitation
Shimming
effect of concentration gradients
effect of sample depth
effect of sample mixing
effect of sample volume
effect of variable temperature gas composition
line shapes resulting from bad shimming
without a lock signal
Sinc distortion
Slice selection
Software for data processing
Solid polymorphs
Solid state 1H NMR
1H spin pairs
Solid state 2H NMR spectroscopy
echoes and Fourier transforms
increasing signal-to-noise ratio
measuring spectral parameters
QCPMG
T1 anisotropy
to determine molecular motions
Solid state NMR vs solution state NMR
Solid state NMR using a probe for liquids
Solid state NMR spectroscopy of quadrupolar nuclides with spin I = n/2
90 degree pulse calibration
baseline correction
enhancement of satellite transitions via the Nyquist sampling theorem
field dependence
Fourier transform of a single rotational echo
satellite transitions
Solution state NMR vs solid state NMR
Solvent effects
improving resolution
Solvent suppression
absolute water suppression
double presaturation
presaturation
watergate
watergate vs presaturation
Spin locking pulses
Spin simulations
butane
ethane
isopropyl groups
quadrupolar line shapes in solids (QUEST)
virtual coupling
Spinning liquid samples
Spinning sideband suppression in MAS spectroscopy
Steady state scans
t1 noise removal in 2D spectra
heteronuclear (tutorial video)
homonuclear (tutorial video)
Textbook recommendation
Thermal noise
TRAPDOR measurements
Triple resonance experiments
13C [2H][1H]
13C [31P][1H]
31P -13C HMQC with 1H decoupling
Variable temperature measurements
temperature calibration (1)
temperature calibration (2)
temperature dependent chemical shifts
temperature gradients
variable temperature gas composition and spectral quality
variable temperature to improve resolution
Video lectures
Video commentary by NMR experts
Video tutorials
1D spectrum phasing
2D spectrum phasing
exponential line broadening
EZ NMR
removing t1 noise from heteronuclear 2D spectra
removing t1 noise from homonuclear 2D spectra
Virtual coupling
Zero Filling
and throwing away noise



Source: University of Ottawa NMR Facility Blog
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