NMR Sparky Yahoo group Re: Regarding processing problem of 2D TOCSY ucsf in sparky

		BioNMR > NMR community > News from other NMR forums
[NMR Sparky Yahoo group] Re: Regarding processing problem of 2D TOCSY ucsf in sparky

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-14-2013, 12:19 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

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

Re: Regarding processing problem of 2D TOCSY ucsf in sparky

Re: Regarding processing problem of 2D TOCSY ucsf in sparky

Hi, His problem was in the nmrPipe processing script and has been resolved. According to me (after having seen his data), what you have suggested would not

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR Sparky Yahoo group] Re: Regarding processing problem of 2D TOCSY ucsf in sparky Re: Regarding processing problem of 2D TOCSY ucsf in sparky Hello Pancham, You can apply a chemical shift correction to your TOCSY spectrum using your ROESY spectrum as a reference: - First, do the peak picking of a few More...	nmrlearner	News from other NMR forums	0	05-13-2013 11:36 AM
[NMR Sparky Yahoo group] Re: Regarding processing problem of 2D TOCSY ucsf in sparky Re: Regarding processing problem of 2D TOCSY ucsf in sparky Hi, Additionally, please post the output of ucsfdata program, which you can find in the bin folder of Sparky installation. Something like, ucsfdata TOCSY.ucsf More...	nmrlearner	News from other NMR forums	0	05-10-2013 07:03 PM
[NMR Sparky Yahoo group] R: [nmr_sparky] Regarding processing problem of 2D TOCSY ucsf in spa R: Regarding processing problem of 2D TOCSY ucsf in spa Hi Pancham, did you check the acquisition parameters you used to record the spectrum? Best, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and More...	nmrlearner	News from other NMR forums	0	05-10-2013 06:58 AM
[NMR Sparky Yahoo group] Regarding processing problem of 2D TOCSY ucsf in sparky Regarding processing problem of 2D TOCSY ucsf in sparky Dear sir/Madam, I am a sparky user and using this software for 2D NMR assignment....I used this software many time...I am facing a problem in ucsf file of 2D More...	nmrlearner	News from other NMR forums	0	05-09-2013 05:37 PM
[NMR Sparky Yahoo group] Re: sparky relaxation fit problem Re: sparky relaxation fit problem Hi Kuen-Phon, You are correct. Thanks for help. Tom ... From: homespuner Subject: Re: sparky relaxation fit problem To: More...	nmrlearner	News from other NMR forums	0	09-15-2012 09:04 AM
[NMR Sparky Yahoo group] Re: sparky relaxation fit problem Re: sparky relaxation fit problem Hi Tom, If I understand correctly, the unit of T2 in your case is mini-second (120 ms = 0.12 s). Therefore the R2 in your example is 1/0.12 = 8.33 s-1. More...	nmrlearner	News from other NMR forums	0	09-14-2012 07:54 AM
[Question from NMRWiki Q&A forum] 3d Tocsy-hsqc mgnetization transfer problem 3d Tocsy-hsqc mgnetization transfer problem Dear All,I acquired a 3d tocsy-hsqc edited on Bruker machine of small protein in micelles with a mixing time of 70ms. The problem is that I do not observe almoust spin system of each aminoacid, in detail I see only cross peaks between NH-HA. I obtained very good results by 3d Noesy-hsqc edited. How can I do to improve the magnetization transfer along the spin system and see all cross peaks? Do you think that this problem is due to the nature?Thank you in advance\ Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	03-06-2012 06:17 PM
[Question from NMRWiki Q&A forum] Data processing and Sparky Data processing and Sparky Dear NMRWikiers, I'm fresh in nmr field and would like to ask couple questions: 1. Our protein has about 132 residues.The NHSQC is well dispersed but many peaks can't be found in CBCANH and CBCACONH. HNCA/HNCOCA + HNCO/HNCACO are planned for backbone assignment. Other people processed data with NMRPipe. The NHSQC peaks can mostly find matching peaks in HNCO/HNCACO, while HNCA/HNCOCA can't be matched (no same resonances can be seen when synchronized). But, many peaks can be seen in HNCA/HNCOCA. I found that the whole scale of 13C axis in HNCA is from 51 to 66 and...	nmrlearner	News from other NMR forums	0	01-26-2012 02:22 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