NMR Discussion Group
Future topics (no specific order):
SOFTWARE RELATED:
automation by macros and au programs
NMRViewJ
Smartnotebook
Sparky
Aria
Marvin
Pecan/Pistacchio
Delphi (electrostatics)
VMD
Amber
NMRWish/Dynamo/MFR
Roland NMR Toolkit
THEORY RELATED:
Relaxation theory (S.Shekar)
angular momentum spectrum (in particular, spin angular momentum) (S.Shekar)
order parameters (S.Shekar)
HARDWARE RELATED:
constant time in NMR
calibration of pulses
PULSE SEQUENCE RELATED:
pulse programming on Varian
automatic setup of HNCACB on Varian
01/16/02
PO for refocussed INEPT
PP for zg and zgpr
assignment: program zgpr and test
01/24/02
PO for reverse refocussed INEPT
PP for inept
assignment: block diagram/PO for HSQC via inept/reverse inept
01/31/02
block diagram/PO for HSQC via inept/reverse inept
PP for 2D-HSQC including cpd decoupling & incrementation via id0
assignment: write PP for 1D-HSQC and test on 300
02/07/02
CPD - what is it? why do it? how to do it? when to do it?
composite pulse decoupling reading list:
R. Freeman, Handbook of NMR, 2nd Ed., pp. 20-29
Croasmun & Carlson, 2D NMR Spectr., pp105-111
Cavanagh et al, pp141-145.
Bruker's XWINNMR Pulse Programming Manual, pp30-36
assignment: run 13C spectrum w/ zg and zgdc
02/14/02
Introduction to Coherence (S.C.Shekar)
recommended reading:
Munowitz "Coherence and NMR"
Wokaum and Ernst, Chem Phys Lett (1977)
assignment: for next meeting, compare result of following 2 sequences:
90x - 180x - acq
90x - 180y - acq
05/09/02
Phase Cycling Part 1 (M.Girvin)
reading list:
Freeman "Handbook of NMR", pp.172-177,198-202
Palmer pp.203-220
Freeman "Spin Choreography", Chapt. 6
assignment: program spin echo and test w/ and w/out phase cycling
test w/ p1 and p2 values set correctly and misset by ~30%
05/23/02
Intro to coherence order and selection (D.Kamen)
reading list:
Freeman "Handbook of NMR" pgs 42-45, 172-177
Freeman "Spin choreography" chpt 6.1
Cavanagh et al "Protein NMR spectroscopy" chpt 2.6, 4.2, 4.3
Bain (1984) J. Mag. Reson. 56, 418-427
Bodenhausen, Kogler, Ernst (1984) J. Mag. Reson. 58, 370-388
assignment: run cosyst on glucose/D2O sample w/ and w/out phase cycling
06/06/02
Rules for creating phase tables for desired coherence selection (D.Kamen)
reading list:
Bain (1984) J. Mag. Reson. 56, 418-427
Bodenhausen, Kogler, Ernst (1984) J. Mag. Reson. 58, 370-388
assignment: workout phase table for NOESY
07/11/02
Gradients and Coherence Selection (R.Krueger)
reading list:
Cavanagh et al "Protein NMR spectroscopy" pp 220-227
07/18/02
more on Gradients and Coherence Selection (R.Krueger)
08/1/02
Using Gradients on the spectrometer (S.Cahill)
gradient hardware
gradient setup and calibration
pulse programming w/ gradients
gradient shimming
magic angle gradients
reading list:
Bruker Avance Grasp Installation/User Manual
Bruker Pulse Programming Manual
Bruker Gradient Shimming on Avance Spectrometers Manual
Warren at al. Science 262, 2005 (1993)
Van Zijl et al. JMR A 113, 265 (1995)
02/11/03
dipolar coupling and alignment tensor (S.Shekar)
reading list:
weak alignment offers new nmr opportunities to study protein structure and dynamics
ad bax
protein science, v12, 1-16 (2003)
order matrix analysis of residual dipolar couplings using singular value decomposition
judit a losconzi, michael andrec, mark w f fischer and james h prestegard
j. magn. resonance, v138, 334-342 (1999)
02/25/03
TROSY (D.Kamen)
reading list: see handout
also see http://www.cyberheadz.com/salzmann/#
03/04/03
CNS refinement with RDC (R.Krueger)
reading list: see handout
04/29/03
water suppression (P.Sorgen)
06/23/03
FHSQC (M.Girvin)
08/25/03
NMRView, the NMRView Navigator and CBCA analysis (S.Poget)
09/08/03
AutoAssign (S.Poget)
9/22/03 & 10/6/03
Shaped Pulses: Theory, Applications and Implementation (D.Kamen)
11/3/03 & 11/6/03
Spin Angular Momentum and NMR and its application to HSQC (S.Shekar)
1/5/04
TROSY-CT-HNCACB - discussion of pulse sequence (S.Shekar)
3/2/04
HNCACB - from pulse sequence to processed dataset (S.Cahill)
3/15/04
the 2nd dimension - what is it, how to get complex data (TPPI, States-TPPI, Echo/AntiEcho), etc. (D.Kamen)
key:
PP = pulse program
PO = product operator