Question from NMRWiki Q&A forum incorrect processing of 2D HSQC in NMRPipe - what is wrong?

		BioNMR > NMR community > News from other NMR forums
[Question from NMRWiki Q&A forum] incorrect processing of 2D HSQC in NMRPipe - what is wrong?

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

04-09-2011, 12:17 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

incorrect processing of 2D HSQC in NMRPipe - what is wrong?

incorrect processing of 2D HSQC in NMRPipe - what is wrong?

i'm trying to process an HSQC by using standard scripts of NMRpipe, and get this:

what is wrong in my processing? at the spectrometer the spectrum looked nice, so it's a matter of processing...

conversion:

bruk2pipe -in ../Bruker/ser -bad 0.0 -aswap -DMX -decim 2080 -dspfvs 20 -grpdly 67.9842 \ -xN 4096 -yN 512 \ -xT 2048 -yT 256 \ -xMODE DQD -yMODE States-TPPI \ -xSW 9615.38 -ySW 2100 \ -xOBS 599.762823 -yOBS 60.780 \ -xCAR 4.707 -yCAR 115.00 \ -xLAB HN -yLAB N \ -ndim 2 -aq2D States-TPPI \ -out ../Data/test.fid -verb -ovprocessing:

nmrPipe -in ./test.fid \| nmrPipe -fn POLY -time \| nmrPipe -fn SINE -c 0.5 -off 0.45 -end 0.98 -pow 2 \| nmrPipe -fn ZF -auto \| nmrPipe -fn FT \| nmrPipe -fn PS -p0 -20.0 -p1 0.0 -di \| nmrPipe -fn EXT -left -sw \| nmrPipe -fn TP \| nmrPipe -fn SINE -c 0.5 -off 0.45 -end 0.98 -pow 2 \| nmrPipe -fn ZF -auto \| nmrPipe -fn FT \| nmrPipe -fn PS -p0 0.0 -p1 0.0 -di \| nmrPipe -fn TP \| nmrPipe -out ./test.ft -ovthanks for the tips!

Nadia

Check if somebody has answered this question on NMRWiki QA forum

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[Question from NMRWiki Q&A forum] HSQC perturbation HSQC perturbation Dear All, I am trying to determine the interaction between 2 proteins. Is there any reference or literature which report the determination of binding constant between 2 proteins in which intensity drop of HSQC cross peaks can be used as the measuring parameter. As when I titrate these 2 proteins only change which I observe is intensity drop. I tried other biophysical techniques to determine binding constant, but results are not satisfactory. Any suggestion would be useful Regards	nmrlearner	News from other NMR forums	1	09-24-2013 02:18 AM
[Question from NMRWiki Q&A forum] what went wrong? what went wrong? a query again? I recorded an DQF on deuterated solid sample. The basic pulse programme taken from bruker, optimised the pulse and kept the proper short delay between the last two 90 pulses? phase cycling is same as mentioned in bruker? I got empty spectrum with very poor diagonal and no cross peaks? what could possibly go wrong ? does these delays depend on higher magnetic field strengths? or pulse imperfections cause collapsed spectrum or empty spectrum? the spectra i recorded on 700 MHz with 14 KHz MAS.	nmrlearner	News from other NMR forums	0	11-18-2011 06:51 PM
[Question from NMRWiki Q&A forum] What's wrong with this spectrum? Bruker TPPI 2D TOCSY What's wrong with this spectrum? Bruker TPPI 2D TOCSY Hi, I think this is probably a basic problem but I'm a bit inexperienced with NMR. I'm just trying to process an ethanol TOCSY spectrum from the biomolecular magnetic resonance data bank, but strange peaks are appearing at the very edge of the data. The spectrum should look like this (processed in SpinWorks): <img src="http://qa.nmrwiki.org/upfiles/12889441489353594.png" width="70%"</img>	nmrlearner	News from other NMR forums	0	11-05-2010 12:20 PM
[Question from NMRWiki Q&A forum] Best pulse sequence for HSQC in Guanidine-HCl Best pulse sequence for HSQC in Guanidine-HCl Hello, I would like to acquire a series of HSQC spectra of an 15N-labeled 12 kDa protein unfolding (over the course of hours) in 3M GuaHCl. I have access to a Varian 600 spectrometer with a conventional probe. Due to the high ionic strength of the sample, tuning and shimming is a little difficult. However, I can record a sort-of-decent HSQC using a WaterGate gradient enhanced WGgNhsqc sequence. I am limited to using a protein concentration of about 250 uM. I've determined the pw90 to be 12.125 at a tpwr of 63. Using WGgNhsqc, the protein...	nmrlearner	News from other NMR forums	0	10-23-2010 07:42 AM
[Question from NMRWiki Q&A forum] data processing by nmrPipe data processing by nmrPipe Hi all,I am very new to nmrPipe. I want to achieve the following steps. It would be very kind if somebody helps.(1) I have a 2D bruker data (t2= 4k points, t1= 32 points) and I want to do Fourier transform in the F2 dimension,phase etc. (2) and then extract the 32 spectra as 1Ds and also convert these 32 spectra in ascii format.(3) fit the peaks with a gaussian or Lorentzian function.(4) integrate the peak and save the integrals and time points as an ascii file.I only managed till the 1st step.Please help..!! Check if somebody has answered this question on...	nmrlearner	News from other NMR forums	0	10-05-2010 02:11 PM
[Question from NMRWiki Q&A forum] Examples of protein degradation eg HSQC? Examples of protein degradation eg HSQC? Anyone know any websites or papers that show protein degradation in an HSQC for example? I wanted to know what to look for in old samples when I have them. Either that, or could someone put one up on the wiki for me to look at? Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	08-22-2010 02:30 AM
[U. of Ottawa NMR Facility Blog] Hsqc - tocsy HSQC - TOCSY There are many different NMR techniques used to probe molecular structure. Two very useful methods are the HSQC (or HMQC) sequence used to obtain heteronuclear coupling correlations and the TOCSY sequence used to look at extended homonuclear coupling correlations. These are among the most widely used pulse sequences by chemists to help elucidate the molecular structure of organic molecules. The sequences can also be combined into a single HSQC-TOCSY sequence which is simply an HSQC followed by a TOCSY spin lock. For the case of 1H and 13C in organic molecules, the HSQC-TOCSY...	nmrlearner	News from NMR blogs	0	08-21-2010 08:15 PM
[Stan NMR blog] Are Bruker and Jeol NMR data wrong? Are Bruker and Jeol NMR data wrong? Recent FID's acquired with Bruker and Jeol spectrometers exhibit an anomalous group delay artifact ... More...	nmrlearner	News from NMR blogs	0	08-21-2010 05:42 PM

« Previous Thread | Next 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