CNS Yahoo group problem in group B factor refinement

		BioNMR > NMR community > News from other NMR forums
[CNS Yahoo group] problem in group B factor refinement

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

08-21-2010, 03:26 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

problem in group B factor refinement

problem in group B factor refinement

Dear CNS users, I am refining a 3.1 A structure (from Molecular Replacement) with CNS 1.3, and after rigid-body and annealing, I wanted to do group B

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[KPWU blog] water refinement in Xplor-NIH water refinement in Xplor-NIH Starting at Xplor-NIH 2.26 (now it’s version 2.29 on Feb. 8th, 2012), official Xplor-NIH package provides an example script doing explicit solvent refinement. The short description made by Xplor-NIH author: ============ wrefine.py: refinement with explicit solvent and full electrostatics. Includesrdcs, noes, jcoupling terms and dihedral restraints. This is awork-in-progress. Please compare with other protocols. In*particular, http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=636&subd=kpwu&ref=&feed=1 Go to KPWU blog to read complete...	nmrlearner	News from NMR blogs	0	02-09-2012 08:16 AM
solution to a basic nmr problem, practice problem 3 solution to a basic nmr problem, practice problem 3 http://i.ytimg.com/vi/mOdABDblqKo/default.jpg solution to a basic nmr problem, practice problem 3 The solution to a good, basic practice nmr and IR problem at Bryn Mawr College by M Nerz From: mnerzsto Views: 4060 http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif http://gdata.youtube.com/static/images/icn_star_full_11x11.gif ...	nmrlearner	NMR educational videos	0	09-14-2011 09:34 PM
[CNS Yahoo group] water refinement problem - broken structure water refinement problem - broken structure Dear all, I'm trying to perform water refinement for the very first time (new CNS user), on an NMR ensemble of CYANA calculated protein structures but the end More...	nmrlearner	News from other NMR forums	0	07-18-2011 09:41 AM
[NMR paper] Structural difference between group I and group II cobra cardiotoxins: X-ray, NMR, an Structural difference between group I and group II cobra cardiotoxins: X-ray, NMR, and CD analysis of the effect of cis-proline conformation on three-fingered toxins. Related Articles Structural difference between group I and group II cobra cardiotoxins: X-ray, NMR, and CD analysis of the effect of cis-proline conformation on three-fingered toxins. Biochemistry. 2005 May 24;44(20):7414-26 Authors: Chen TS, Chung FY, Tjong SC, Goh KS, Huang WN, Chien KY, Wu PL, Lin HC, Chen CJ, Wu WG Natural homologues of cobra cardiotoxins (CTXs) were...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis. J Biol...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[CNS Yahoo group] Re: problem in group B factor refinement Re: problem in group B factor refinement Actually, group B-factor refinement now also includes restraints when using the new "refine.inp" task file in v1.3. I suggest you try various values for the More...	nmrlearner	News from other NMR forums	0	08-21-2010 03:26 PM
[CNS Yahoo group] Re: problem in group B factor refinement Re: problem in group B factor refinement Grouped B-factor refinement doesn't work well because it is unrestrained in nature and allows for discontinuites in B-factors of covalently bonded atoms. Just More...	nmrlearner	News from other NMR forums	0	08-21-2010 03:26 PM
structure refinement after cyana Can anybody tell me, how to energy minimize a CYANA calculated average structure. I used model_minimize.inp from CNS, but is there any other method generally used by the CYANA users. Also, how can I get the bonds, impropers and angle violation (rmsds) information on the CYANA calculated structures. Does CYANA has any program to do it. Please help me with it. Thank you.	sarun	NMR Questions and Answers	0	11-20-2008 03:41 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