NMR Sparky Yahoo group Re: R: [nmr_sparky] noe distance restraints

		BioNMR > NMR community > News from other NMR forums
[NMR Sparky Yahoo group] Re: R: [nmr_sparky] noe distance restraints

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

09-29-2012, 11:56 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,778

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: R: [nmr_sparky] noe distance restraints

Re: R: [nmr_sparky] noe distance restraints

Hi Marco, Thanks that is helpful. Here is what i did and it looks like it is working. i used thexf command and it gives you a window where you can input the

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR Sparky Yahoo group] R: [nmr_sparky] noe distance restraints R: noe distance restraints Hi Werkawi, the peak list you generate with lt after integration can be saved in a .list file. This file can be the input for some program, in python or the More...	nmrlearner	News from other NMR forums	0	09-28-2012 04:15 AM
[NMR Sparky Yahoo group] noe distance restraints noe distance restraints Hello Sparky users, i want to generate distance retraints from the Noe peak volumes i have. sofar i have integrated all the peaks and i tried to classify them More...	nmrlearner	News from other NMR forums	0	09-28-2012 04:15 AM
[NMR Sparky Yahoo group] R: [nmr_sparky] Re: distance constraints from NOESY crosspeaks R: Re: distance constraints from NOESY crosspeaks A single spectrum at 300 ms contains a lot of spin diffusion. It's good to assign DNA/RNA not for constraints. Try to use something like 50 ms instead. Marco More...	nmrlearner	News from other NMR forums	0	02-13-2012 02:34 AM
[Question from NMRWiki Q&A forum] Generate inter-proton distance restraints from an X-ray structure Generate inter-proton distance restraints from an X-ray structure Hello, Does anyone know of any program that can generate inter-proton distance restraints from an X-ray structure?I was able to use Molmol to generate dihedral angles. MolMol can also generate inter-atom distances, however, I could not figure out how to just generate 1H-1H distances. I have a total of 50,000 inter-atom distance (H-H, C-O, C-N...all types). Any help is highly appreciated. Winston	nmrlearner	News from other NMR forums	0	04-25-2011 03:43 AM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. J Am Chem Soc. 2011 Apr 4; Authors: Ryabov Y, Schwieters CD, Clore GM (15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...	nmrlearner	Journal club	0	04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja201020c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ	nmrlearner	Journal club	0	04-05-2011 10:37 AM
[NMR paper] Automated NOESY interpretation with ambiguous distance restraints: the refined NMR so Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol. 1997 Jun 13;269(3):408-22 Authors: Nilges M, Macias MJ, O'Donoghue SI, Oschkinat H We have used a...	nmrlearner	Journal club	0	08-22-2010 03:03 PM
Distance restraints for structure determination Distance restraints for structure determination Experimentally derived parameters for protein structure determination, Part 1: nOe distance restraints. Lecture by Dr. Matthew Cordes from University of Arizona. More...	nmrlearner	General	0	08-16-2010 03:50 AM

« 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