BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from other NMR forums
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
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


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 06-12-2012, 11:25 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Gradient strength recalculation

Gradient strength recalculation

Iam bit stuck with % z gradient calculation used in Bruker pulse programs. In some instruments (Varian) they use as short as 200us for some gradient pulses, but in Bruker, they fix the length of all the gradient pulses as constant (say 500 us) and vary the gradient strength accordingly.

Hence, is there any easy way to convert a gradient pulse of say 17 G/cm applied for 0.5 ms to 'x' G/cm for 1ms.(where 'x' is the new gradient strength for 1ms).

Once this conversion is completed,the next step would be to calculate the gradient % which i think is the ratio of ('x' (G/cm)*100)/Maxgradamplitude, where Maxgradamplitude is the maximum G/cm specified for a spectrometer (e.g. 70 G/cm for an 800 MHz).

(I read from Dr.James Keeler notes that the sum of the phase of the coherence before and after the application of a pair of z gradient pulses should be zero, for an appropriate coherence to be selected. The book also suggests an handy formulae (s1*Bg1t_1)/(s_2Bg2*t2) = -p1/p2; where s1,s2 are shape factors of gradient pulses used for coherence selection. Bg1,Bg2 are the gradient field strength of first and second gradient pulse, t1,t2 are the time period for each applied pulse and p1 and p2 are the coherence before and after the gradient pulses, respectively. But this formulae requires the complete coherence transfer pathway to be elucidated.On the other hand, the published sequence would have considered all these details while providing the strength and delays of gradient pulses. So is it possible to take advantage of the already existing information and make the conversion for desired delays in a simplied way.)



Check if somebody has answered this question on NMRWiki QA forum
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[KPWU blog] [PyMOL] gradient background color
gradient background color Starting at *PyMOL 1.4, *single color for the background is no longer the only choice. By using 3 PyMOL commands, the gradient background color can be easily shown. The only thing users have to know is that command “ray” doesn’t support this gradient color yet. So if you type “ray” in the pymol terminal , http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=619&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete post.
nmrlearner News from NMR blogs 0 11-15-2011 11:36 PM
[Question from NMRWiki Q&A forum] Problem with the gradient shimming
Problem with the gradient shimming Dear Friends, I've recently encountered a problem with gradient shimming that has never happened to me before. I can't clearly determine what caused it but it certainly didn't involve anybody manipulating with the probe. Here's the symptom: when running the gmapz experiment, the Z-profiles (before and after gradient) look like this: http://img833.imageshack.us/img833/2213/zprofilef.png As you can see the second profile (after the gradient) is distorted at the left edge (more or less severely, depending on a sample - here it's just a tiny "step")....
nmrlearner News from other NMR forums 0 10-11-2011 06:35 PM
[Question from NMRWiki Q&A forum] gradient shim map question
gradient shim map question Does anyone know for sure if a shim map is off center slightly left in a negative direction...and I assume it is a centering issue do you whether it would be probe up/down? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 10-19-2010 06:35 PM
[Question from NMRWiki Q&A forum] How do you port pulse sequences to different field strength?
How do you port pulse sequences to different field strength? Hi, when you set up a pulse sequence at a different magnet field strength - starting with an existing set of parameters - what do you look at? Does length of shaped pulses always need to be changed? What pulse lenghts need to be adjusted? When it is necessary to re-build RF waveforms - for what kinds of pulses?
nmrlearner News from other NMR forums 0 08-22-2010 02:30 AM
[NMRwiki tweet] nmrwiki: How do you port #NMR pulse sequences to different field strength? #spectrosc
nmrwiki: How do you port #NMR pulse sequences to different field strength? #spectroscopy http://qa.nmrwiki.org/question/148/ nmrwiki: How do you port #NMR pulse sequences to different field strength? #spectroscopy http://qa.nmrwiki.org/question/148/ Source: NMRWiki tweets
nmrlearner Twitter NMR 0 08-22-2010 01:49 AM
[U. of Ottawa NMR Facility Blog] Gradient Spin Echoes for Selective Excitation
Gradient Spin Echoes for Selective Excitation Shaped excitation pulses can replace the non-selective hard pulses typically used in a one-pulse measurement to achieve selective excitation. Another method of achieving selective excitation is the gradient spin echo using a selective 180° pulse. This technique is demonstrated in the figure below. http://4.bp.blogspot.com/_5wBTR2kKTqA/S_UxeG5oXdI/AAAAAAAAAzc/BHWef-Tse7s/s400/grad_spin_echo.jpgA non-selective hard 90°x pulse is first given followed by a pair of identical pulsed field gradients sandwiching a soft selective 180° pulse about the y...
nmrlearner News from NMR blogs 0 08-21-2010 08:15 PM
Gradient Coils
http://farm4.static.flickr.com/3304/3268388270_9f03dd66e6.jpg Gradient Coils More...
nmrlearner NMR pictures 0 08-18-2010 01:12 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:25 AM.


Map