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Announcing version 1.3 (general release) of the software:
Crystallography & NMR System (CNS)
(copyright 1997-2010, Yale University)
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Information about the software and instructions for downloading
the most recent version are available at:
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************ http://cns-online.org****************
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The software is available for download, free-of-charge, by all
academic (non-profit) users.
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Installation instructions and documentation can be found in:
$CNS_SOLVE/doc/html/cns_solve.html
once you have downloaded and installed the software.
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Do not distribute CNS to third parties without approval. By
downloading the software you agree to the License in the FTP
directory.
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While this new version is compatible with version 1.2 input files it
is highly recommended that you use the new input files and
modules in conjunction this new version of CNS. The http://cns-online.org
website is now pointing to the new 1.3 version by default.
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Attached release notes for CNS version 1.3:
=======================================================================
=
= Crystallography & NMR System
=
= A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
= P.Gros, R.W.Grosse-Kunstleve,J.-S.Jiang,J.M.Krahn,
= J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
= L.M.Rice, G.F.Schroeder, T.Simonson, G.L.Warren.
=
= Copyright (c) 1997-2010 Yale University
=
=======================================================================
Program: CNS
Version: 1.3
Patch level: 0
Status: general release
Changes for version 1.3
------------------------
Summary of major changes and new features for version 1.3
---------------------------------------------------------
- DEN method for low resolution refinement. See the new tutorial:
Structure refinement at low resolution (below ~ 3.5 A resolution).
http://cns-online.org/v1.3/tutorial/refinement_low_resolution/den_refinement/text.html
(Reference:
G.F. Schroeder, M. Levitt, and A.T. Brunger, Super-resolution
biomolecular crystallography with low-resolution data, Nature 464,
1218-1222, 2010)
- Simulations of single molecule FRET-derived distances and docking
calculations with FRET-derived distances. See the new tutorial:
Single molecule FRET.
http://cns-online.org/v1.3/tutorial/fret/docking_calculations/text.html
http://cns-online.org/v1.3/tutorial/fret/dye_simulations/text.html
http://cns-online.org/v1.3/tutorial/fret/fret_distribution_calculations/text.html
(References:
M. Vrljic, P. Strop, J.A. Ernst, R.B. Sutton, S.Chu, A.T. Brunger,
Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+
-triggered
vesicle fusion, Nature Structural and Molecular Biology 17, 325-331, 2010;
U.B. Choi, P. Strop, M. Vrljic, S. Chu, A.T. Brunger, K.R. Weninger,
Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion
complex.
Nature Structural and Molecular Biology 17, 318-324, 2010).
- Automatic generation ("on-the-fly") of molecular topology (mtf)
files (see the tutorial in Generating PDB and MTF files). Note that this
new feature has required that wildcards are not allowed anymore in
the topology "link" files. Also, all residues need to be defined in
the topology files.
- Greatly expanded, general refinement script file
(inputs/xtal_refine/refine.inp and inputs/xtal_twin/refine_twin.inp)
for most refinement tasks, including positional (xyz), B-factor refinement,
simulated annealing, and DEN refinement. The new script also
writes 2Fo-Fc and Fo-Fc electron density maps in CNS/X-PLOR format as well
as a coefficient file (.hkl) that can be read directly by Coot, version
0.6.1, or
later (or by the CNS script fourier_map.inp for B-factor sharpening).
- new all-hydrogen topology and parameter files (protein-allhdg5-4*, and
dna-rna-allatom-hj-opls.*). These files are used for NMR structure
determination, but they can also be used for X-ray structure
refinement to include all hydrogen atoms in the refinement (see the new
tutorials on this topic). Electrostatics can also be used with these new
files.
http://cns-online.org/v1.3/tutorial/refinement_all_hydrogen_atoms/text.html
http://cns-online.org/v1.3/tutorial/refinement_all_h_electrostatics/text.html
(Reference: J.P. Linge, M.A. Williams, C.A.E.M. Spronk, A.M.J.J. Bonvin,
M. Nilges, Refinement of protein structures in explicit solvent.
Proteins 50, 496-506, 2003).
- New and updated refinement tutorials, including a tutorials
for refinement at low resolution, refinement of ribosome structures,
refinement with all hydrogen atoms, and weight optimization by Rfree.
- Protein, nucleic acid, and carbohydrates topology files
conform with the most recent PDB standard.
- Automatic linkage detection for N-linked carbohydrates based on distance.
- Hybrid-36 for atom serial numbers for PDB files produced by CNS and
support for hybrid-36 for the "resid" field (see tutorial on
Coordinate fles).
- Generation of topology and parameter files from CIF files with new
cns_import_cif utility written by Joseph M. Krahn. See the tutorial
on "Conversion of CIF files into CNS parameter and topology files.
http://cns-online.org/v1.3/tutorial/generate/tools/import_cif.html
- Performance improvements for torsion angle topology generation
for very large systems such as ribosome crystal structures.
- a CNS wiki:
http://cns-online.org/wiki/index.php/Main_Page
Contributions are encouraged and appreciated.
Your feedback is greatly appreciated!
(detailed list of changes are in the Changes file in the CNS root directory)
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atbweb.stanford.edu
Email: brun...@stanford.edu
Phone: +1 650-736-1031
Fax: +1 650-745-1463
