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  
Unread 10-31-2012, 10:14 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,187
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 Varian VNMRJ 2.2D standard experiments

Varian VNMRJ 2.2D standard experiments

Hey folks, I was wondering if anyone else has had any issues with the experiments/pulse sequences that came standard in the VNMRJ software? I am running VNMRJ 2.2D on Red Hat Enterprise, but have yet to have much success with any experiment outside of standard 1H, 13C, 19F, and 31P. Lately we have been trying to run C13DEPT, C13APT, (HC)HMBC, (HC)HSQC, and HETCOR, and have come up with nothing usable. The DEPT experiment produces the 4 expected spectra, but three are blank/noise and the fourth is just a standard carbon scan; the APT was promising, but I noticed a peculiarity about it: if I printed out the c13 spectra, the peaks were positive/negative as expected until about halfway through, where the spectra repeated itself, only upside down and in the opposite direction (as if it were simply rotated 180 degrees around the center of the spectra); HMBC, HSQC, and HETCOR all ran, but when I try to open them, I only get the message "LP analysis failed." Any attempt to display either fid or the 2D comes up fruitless (after wft each fid independently, selecting a 2D display returns the message "No 2D data in data file"). I have been able to open the HETCOR in a separate software suite (ACD labs Spectrus Processor), and the spectra there are horrific: the proton spectra is a poorly defined mess of peaks mirror imaged around the tof, and the carbon scan comes up as simply noise.

Any help you can give for how to tweak the parameters or pulse sequence is appreciated. I feel like my job depends on it!



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
[Question from NMRWiki Q&A forum] eretic standard sample
eretic standard sample I have recently set up the eretic sample concentration measurement experiment experiment on our AvanceIII instrument. It seems to work well but the accuracy of the technique depends on the standard sample used to calibrate, I used the Bruker 48.5 mM triphenylphosphate standard since it would be good for 1H, 13C and 31P and its concentration is known fairly precisely however I have been advised that these standards from bruker use thinner walled tubes than most of my users purchase and that therefore they have a different volume and this will lead to errors to...
nmrlearner News from other NMR forums 0 06-19-2012 01:38 PM
[CNS Yahoo group] Re: A standard way to install CNS in linux (Ubuntun) without mistake
Re: A standard way to install CNS in linux (Ubuntun) without mistake Dear Ed, the precompiled CNS binaries does not work for NMR, because CNS needs to be compiled with modified source code for using it with ARIA and HADDOCK. More...
nmrlearner News from other NMR forums 0 06-10-2012 05:38 PM
[CNS Yahoo group] A standard way to install CNS in linux (Ubuntun) without mistake
A standard way to install CNS in linux (Ubuntun) without mistake Dear all: After spending the whole night and solving all compiling mistakes (like failure of gfortran,g77,pgf95 et al), i just figure out how to install CNS More...
nmrlearner News from other NMR forums 0 06-08-2012 08:47 PM
[CNS Yahoo group] A standard way to install CNS in linux (Ubuntun) without mistake
A standard way to install CNS in linux (Ubuntun) without mistake Dear all: After spending the whole night and solving all compiling mistakes (like failure of gfortran,g77,pgf95 et al), i just figure out how to install CNS More...
nmrlearner News from other NMR forums 0 06-08-2012 08:31 AM
[NMRwiki tweet] nmrwiki: How to fix this shimdriver error in vnmrj? #nmrhttp://qa.nmrwiki.org/question/232/problems-about-vnmrj-23a-2-shimdriver
nmrwiki: How to fix this shimdriver error in vnmrj? #nmrhttp://qa.nmrwiki.org/question/232/problems-about-vnmrj-23a-2-shimdriver nmrwiki: How to fix this shimdriver error in vnmrj? #nmrhttp://qa.nmrwiki.org/question/232/problems-about-vnmrj-23a-2-shimdriver Source: NMRWiki tweets
nmrlearner Twitter NMR 0 03-04-2011 02:12 AM
[NMRwiki tweet] nmrwiki: How to change thickness of #NMR lines in VNMRJ?http://qa.nmrwiki.org/question/230/problems-about-vnmrj-23a3-fid-display-style
nmrwiki: How to change thickness of #NMR lines in VNMRJ?http://qa.nmrwiki.org/question/230/problems-about-vnmrj-23a3-fid-display-style nmrwiki: How to change thickness of #NMR lines in VNMRJ?http://qa.nmrwiki.org/question/230/problems-about-vnmrj-23a3-fid-display-style Source: NMRWiki tweets
nmrlearner Twitter NMR 0 03-04-2011 02:12 AM
[NMRwiki tweet] nmrwiki: How to turn ON fid for shimming in VNMRJ? #nmrhttp://qa.nmrwiki.org/question/231/problems-about-vnmrj-23a-1shimming
nmrwiki: How to turn ON fid for shimming in VNMRJ? #nmrhttp://qa.nmrwiki.org/question/231/problems-about-vnmrj-23a-1shimming nmrwiki: How to turn ON fid for shimming in VNMRJ? #nmrhttp://qa.nmrwiki.org/question/231/problems-about-vnmrj-23a-1shimming Source: NMRWiki tweets
nmrlearner Twitter NMR 0 03-04-2011 02:12 AM
[Stan NMR blog] Passive Electronic Components: Standard Values
Passive Electronic Components: Standard Values Values of resistors, capacitors and inductors as defined by IEC 63. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 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 12:59 AM.


Map