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
[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. Includes*rdcs, noes, jcoupling terms and dihedral restraints. This is a*work-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
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02-09-2012 08:16 AM
[CNS Yahoo group] refinement of large low resolution structure
refinement of large low resolution structure
Hi all, I have a structure at 2.65A that I'm in the process of refining. It's a complex that has ~1100 residues total, and what looks like a fair amount of
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nmrlearner
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10-22-2010 07:36 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins.
Related Articles NMR chemical shifts and structure refinement in proteins.
J Biomol NMR. 1993 Sep;3(5):607-12
Authors: Laws DD, de Dios AC, Oldfield E
Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
nmrlearner
Journal club
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08-22-2010 03:01 AM
[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
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nmrlearner
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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
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nmrlearner
News from other NMR forums
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08-21-2010 03:26 PM
[CNS Yahoo group] 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
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nmrlearner
News from other NMR forums
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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
CNS water refinement scripts from RECOORD website
CNS scripts for water refinement of NMR-derived protein structures are available on the RECOORD website.
Reference:
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
Aart J. Nederveen 1, Jurgen F. Doreleijers 2, Wim Vranken 3, Zachary Miller 4, Chris A.E.M. Spronk 5, Sander B. Nabuurs 5, Peter Güntert 6, Miron Livny 4, John L. Markley 2, Michael Nilges 7, Eldon L. Ulrich 2, Robert Kaptein 1, Alexandre M.J.J. Bonvin 1 *
1Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
2Center...