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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 08-06-2015, 10:24 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,778
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 Long BioPack calibration run time

Long BioPack calibration run time

I am running BioPack on a Varian INOVA 800MHz on a newly aquired 13C15N1H sample and I have come across an issue that I was wondering if anyone could shed some light on.

When it got to the CBCAcoNH, the experiment it setup to calibrate the phi7cal is set to take ~3hours! with nt=520. I have reasonable signal (my sample is 0.8mM), so why is it doing this? Does it determine a S/N value at somepoint that maybe went awry?

I set up BioPack in the following manner:

create new experiment, load ghn_co and set parameters:

cexp(100) jexp100 ghn_coTROSY='n' gzlvl1=10000 gzlvl2=9600 mag_flg='n' np=1024, tpwr=62, pwClvl=63, pwNlvl=62set pw and tof as manually determined

Main Menu ->Setup->Proteins->Manag Probe Files=> Update Probe Files with these Parameters

Back->Calibrate->Full

Thanks for any insights!



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
[U. of Ottawa NMR Facility Blog] Radiation Damping and Pulse Calibration
Radiation Damping and Pulse Calibration Radiation damping causes broadening in the NMR resonances of very strong signals (such as the 1H signal of pure water) as a result of currents induced in the coil from the strong transverse magnetization. Radiation damping can also produce asymmetry and phase irregularities in the affected resonances. These problems make pulse calibration by the standard nutation curve problematic when very strong signals are used for the calibration. The left-hand panel (black) of the figure below shows the standard 1H nutation curves for 0.1% H2O in D2O (bottom)...
nmrlearner News from NMR blogs 0 06-25-2015 05:28 AM
[Question from NMRWiki Q&A forum] 15N 90 degree hard pulse calibration
15N 90 degree hard pulse calibration Greetings, I want to ask for some advice in matter of 15N hard pulse calibration on Bruker machines. I'm working on Avance DRX 500 with 5mm TBI probe. This calibration is easy to made if 15N urea is avaible, but I don't have opportunity to use this compound. I have in my stable horses as follows: methylamine hydrochloride (99% 15N) ammonium chloride (99,9% 15N) aniline (15N >99%) sodium nitrite (99% 15N) I tried to use first two salts in DMSO-d6. Unfortunately I couldn't obtain proton spectrum with multiplet structure that is needed for pulse...
nmrlearner News from other NMR forums 0 08-19-2014 11:21 AM
[Question from NMRWiki Q&A forum] Calibration of a Bruker NMR probe
Calibration of a Bruker NMR probe I've received a loaner probe from Bruker while ours is being repaired but I'm not getting any timely response on instructions on calibrating it for use. Anyone have a resource or documentation? Thanks, Ken
nmrlearner News from other NMR forums 0 06-16-2012 06:01 AM
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data Yi Xue, Joshua M. Ward, Tairan Yuwen, Ivan S. Podkorytov and Nikolai R. Skrynnikov http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja206442c/aop/images/medium/ja-2011-06442c_0001.gif Journal of the American Chemical Society DOI: 10.1021/ja206442c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/NvRRKHU2H3k
nmrlearner Journal club 0 01-28-2012 05:27 AM
[Question from NMRWiki Q&A forum] 2D Filtered NOESY/TOCSY on Varian Biopack
2D Filtered NOESY/TOCSY on Varian Biopack I am attempting to run some filtered NOESY and TOCSY experiments using sequences in the Varian Biopack - CNfiltocsy and CNfilnoesy. The experiments seem to run fine, but when overlaying the processed spectra something seems odd - the TOCSY crosspeaks are not present in the NOESY spectra and vice-versa. Does anyone know why this might be the case? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 12-20-2010 01:52 AM
[Question from NMRWiki Q&A forum] Varian Biopack pulse sequences for intermolecular NOEs
Varian Biopack pulse sequences for intermolecular NOEs Hi All, I'm trying to set up some experiments to determine intermolecular NOEs in a peptide:protein complex. At the moment from looking at the Biopack library, I have found 4 pulse sequences which will do this and each provide different information (gnoesyNhsqc_CN, gnoesyNhsqc_NN, gnoesyChsqc_CC and gnoesyChsqc_NC). Would people recommend using a combination of all four of these experiments to determine the intermolecular NOEs for use in structure calculations? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 08-22-2010 02:30 AM
[NMRwiki tweet] nmrwiki: know #varian biopack pulse sequences for intermolecular noes? #nmr #chemistr
nmrwiki: know #varian biopack pulse sequences for intermolecular noes? #nmr #chemistry http://qa.nmrwiki.org/question/154/ nmrwiki: know #varian biopack pulse sequences for intermolecular noes? #nmr #chemistry http://qa.nmrwiki.org/question/154/ Source: NMRWiki tweets
nmrlearner Twitter NMR 0 08-22-2010 01:49 AM
[U. of Ottawa NMR Facility Blog] Temperature Calibration - An Alternative Method
Temperature Calibration - An Alternative Method It is well known that the actual temperature of a sample in an NMR probe is not necessarily the same as that read from the variable temperature unit on the spectrometer. This is because the thermocouple used by the variable temperature unit is below the sample tube and not in the center of the rf coil where the NMR measurements are made. One normally must make a calibration plot for the actual temperature vs. the set temperature. For temperatures above room temperature this can be done by employing the known temperature dependent chemical...
nmrlearner News from NMR blogs 0 08-21-2010 08:15 PM



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 12:44 PM.


Map