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==================================================================
Announcing version 1.2 (general release) of the software:
Crystallography & NMR System (CNSsolve)
(copyright 1997-2007, Yale University)
==================================================================
Information about the software and instructions for downloading
the most recent version are available at:
**************************************************
************ http://cns.csb.yale.edu *************
**************************************************
The software is available for download, free-of-charge, by all
academic (non-profit) users.
------------------------------------------------------------------
Installation instructions and documentation can be found in:
$CNS_SOLVE/doc/html/cns_solve.html
once you have downloaded and installed the software.
------------------------------------------------------------------
Please cite the following reference for CNSsolve in
publications:
Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P.,
Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M.,
Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.
Crystallography & NMR system: A new software system for
macromolecular structure determination,
Acta Cryst. (1998) D54, 905-921.
Please cite additional original papers when using specific
methods.
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Do not distribute CNSsolve to third parties without approval. By
downloading the software you agree to the License in the FTP
directory.
------------------------------------------------------------------
Attached release notes for CNSsolve version 1.2:
=======================================================================
= =
= 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.Kuszewski, M.Nilges, =
= N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren =
= =
= Copyright (c) 1997-2007 Yale University =
= =
=======================================================================
Program: CNSsolve
Version: 1.2
Patch level: 0
Status: general release
Changes for version 1.2
-----------------------
Program:
- default number of atoms set to 200,000
- atom number can go up to 999999 in the PDB files produced by CNS
by using some of the 'ATOM' and 'HETATM' record if the number goes
above 99999
- fixed bug in treatment of HL coefficients for remapping of reflections
for some spacegroups
- installation files for x86_64 linux platforms (using gfortran or ifort)
- installation files for Intel Mac systems (using ifort)
- installation files for Mac PPC systems
- Intel Mac OSX binary distribution
- all known dynamic memory pointer problems fixed
- Windows binary installation removed
- use of sort function updated in cns_solve_env file
- use of sed updated in cns_solve_env file
- consolidated distribution into one tar file
- updated output files in the test directory
- generic CPU_TIME subroutine call for Intel Mac OSX, Intel X86_64, and Intel
i686
- replaced -tpp7 option with -axP for Intel X86_64 and Intel i686
- removed "norm" function from atom property do command
- enabled DISP=KEEP for CLOSe statement on linux and mac intel versions
Task files:
- updated bulk solvent model and scale factor calculations (developed for robust
refinement and low resolution applications):
all refinement and model map task files:
- new solvent model grid search and solrad/shrink search
- absolute grid size range for solvent mask calculation is forced
to be between [sqrt 3*0.577 = 1] 0.57 and 0.9 A
- removed low_res_bscale parameter, the low resolution limit is used
- reported anisotropic tensor in coordinate files is now Ucart (not
Ucif as before)
- fixed anisostropic B-scaling symmetry restraints in all modules (scalef,
- removed "anisotropic_fixed_isotropic" option throughout all script files
- fixed method to remove isotropic component from anisotropic B-tensor
- new bulk solvent and scaling routines in structure deposition files:
xtal_pdbsubmission/xtal_pdbsubmission.inp
xtal_mmcif/deposit_mmcif.inp
- fixed bug when a structure has a lower resolution that th default Wilson
limit:
xtal_pdbsubmission/xtal_pdbsubmission.inp
- automatic and fixed bulk solvent parameter options:
all refinement and model map task files
- new automatic sharpening B-factor determination script file:
xtal_util/bsharp.inp
- B-sharpening parameter introduced into various map files:
xtal_util/fourier_map.inp
xtal_refine/model_map.inp
sa_omit_map.inp
composite_omit_map.inp
fo-fo_map.inp
- corrected local real space correlation coefficient computation:
xtal_refine/model_map.inp
composite_omit_map.inp
water_delete.inp
xtal_twin/model_map_twin.inp
- fixed Wilson calculation for very large structures
xtal_util/bsharp.inp
analyse.inp
scale.inp
- fixed bug in water picking if no sites are found:
xtal_refine/water_pick.inp
xtal_twin/water_pick_twin.inp
- duplicate water parameters no longer read in water picking:
xtal_refine/water_pick.inp
xtal_twin/water_pick_twin.inp
- introduced optional B-factor reset option:
xtal_refine/refine.inp
- increased the default number of cycles to 3:
xtal_refine/refine.inp
- removed multiple coordinate file reading option:
xtal_refine/composite_omit_map.inp
sa_omit_map.inp
model_map.inp
xtal_util/model_phase.inp
xtal_twin/model_map_twin.inp
- removed option to write separate bulk solvent model structure factors:
xtal_util/model_phase.inp
- increased the default number of macrocycles to 15:
xtal_phase/mad_phase.inp
- changed the default output array name to fmodel and added warning if fcalc
is used as the name:
xtal_util/model_fcalc.inp
- increased maxtree to 20:
in all torsion angle input files
- Ucart reported instead of Ucif:
heavy atom site refinement scripts
- modified Patterson map task files to use ascii map files instead of
binary map files:
xtal_patterson/predict_patterson.inp
patterson_map.inp
- updated density_modify.inp task file:
mask completion
warning about absolute scaling of input amplitudes
- new input file to calculate structure factors from an EM reconstruction map:
xtal_util/em_map_to_hkl.inp
HTML Documentation:
- updated installation documentation
Modules:
- fixed bug in siterefine module: FOMs for centrics were non-zero for SAD
phasing
- removed "anisotropic_fixed_isotropic" option throughout all modules:
scaleftarget, scaleftarget2, scale_and_solvent
- new module: scale_solvent
- new module for automatic determination of FFT gridding parameters
fft_parameter_check:
- determines optimum B-factor increment
- ELIM parameter is automatically increased for atomic resolution structures
(starting at 1.4 A and higher)
- default ELIM value is set to 8
- grid size is set to the min of ( 1, d_min * 0.3333 )
Libraries:
- conformational database library files incorporated into distriubtion
libraries/confdb/*
Utilities:
- modified Patterson map programs to use ascii map files instead of binary
map files:
utils/PSmap*
============================================================================
--
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atb.slac.stanford.edu
Email: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
