A quick guide to compiling ARIA 2.2, CNS 1.21, AQUA 3.2 and PROCHECK, under Ubuntu Karmic 9.10 (32-bit) If you use Gentoo linux, you can find aria under sci-chemistry (masked by ~x86). Procheck is in the science overlay (see the layman and overlays documentation). Aqua has to be installed manually at the time of writing this [...]
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
nmrlearner
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11-24-2010 09:25 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
nmrlearner
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11-24-2010 08:49 PM
[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding?
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down.
In the end there is a message
****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look?
edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
nmrlearner
News from other NMR forums
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11-02-2010 11:22 PM
[NMR paper] AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Related Articles AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
J Biomol NMR. 1996 Dec;8(4):477-86
Authors: Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a...
nmrlearner
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08-22-2010 02:20 PM
Structure Calculation Using CS-DP ROSETTA from NESG Wiki
Structure Calculation Using CS-DP ROSETTA
This is a copy of instructions for CS-DP Rosetta from NESG Wiki that was created on 8/20/19. Please go to the original post at http://www.nmr2.buffalo.edu/nesg.wiki/Structure_Calculation_Using_CS-DP_ROSETTA
for a more up-to-date version.
Introduction
The CS-DP-Rosetta approach merges the ideas of model generation using CS-Rosetta with model filtering by agreement to NOESY data via the DP-score from the RPF program to generate high accuracy protein structures. This hybrid approach uses both local backbone chemical shift data...
markber
BioNMR Wiki
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08-20-2010 12:22 PM
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
premprakash
NMR Questions and Answers
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03-29-2007 02:33 PM
PASD: auto NOE assignment & structure calculation
Completely Automated, Highly Error-Tolerant Macromolecular Structure Determination from Multidimensional Nuclear Overhauser Enhancement Spectra and Chemical Shift Assignments
Kuszewski, J.; Schwieters, C. D.; Garrett, D. S.; Byrd, R. A.; Tjandra, N.; Clore, G. M.;
J. Am. Chem. Soc. 2004; 126(20); 6258-6273
http://pubs.acs.org/isubscribe/journals/jacsat/126/i20/figures/ja049786hn00001.gif
Abstract:
The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser...
Compiling Aria2, CNS, procheck and aqua for NMR structure calculation
Linear Mode
