CNSsolve general release 1.1

CNS cns at cns.csb.yale.edu
Thu Aug 2 20:44:47 EST 2001


==================================================================

Announcing version 1.1 (general release) of the software:

             Crystallography & NMR System (CNSsolve)
             (copyright 1997-2001, Yale University)

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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.

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Attached release notes for CNSsolve version 1.1:

=======================================================================
=                                                                     =
=                  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) 1997-2001 Yale University                        =
=                                                                     =
=======================================================================

            Program: CNSsolve
            Version: 1.1
        Patch level: 0
             Status: general release


Changes for version 1.1
-----------------------

Program:

- fixed bug in maximum likelihood targets when using anomalous data
- fixed bug in fast translation search that could permit special
  positions to be searched during molecular replacement
- modified DEC Alpha installation to deal with treatment of backslash
  by the latest Compaq Fortran compiler
- modified Linux installations to only use -malign-double flag on x86 based
  machines
- added test in code to try to catch bug in fast math library on some SGIs
- added new Makefile options for compilation with fast math library on SGIs
- added Makefile for Compaq compilers running under Linux on Alpha platforms

HTML Interface:

- updated CGI scripts to account for treatment of undef in the latest
  development version of PERL

HTML Documentation:

- added flowcharts (in PDF format) for phasing tutorials
- added guidelines for MAD and SAD phasing tutorials
- added information to the FAQ
    - possible problems with RedHat 7 on Linux systems
    - problems with fastmath library under Irix 6.5 on R5000 SGI systems
- added recent papers to bibliography

Task files:

- fixed major bugs in:
    xtal_refine/composite_omit_map.inp (map was made over most of unit cell
                                        instead of around selected atoms)
    auxiliary/ncs.def (incorrect application of skew matrix)
    xtal_refine/refine.inp (atom-based parameter corrections were not 
                            applied - cis-peptides were not recognized)
    xtal_util/model_phase.inp (incorrect combination of structure factors from
                               model and bulk solvent)

- fixed minor bugs in:
    general/neighbours.inp (environment option could not be enabled
                            from HTML interface)
    xtal_phase/mad_phase.inp (f'/f'' values not reported as absolute values in
                              summary file)
    xtal_mmcif/deposit_mmcif.inp (incorrect binwise free R-values reported)

- changes to:
    xtal_util/analyse.inp (output correlation of anomalous signal between 
                           different datasets as both a matrix and by
                           resolution - useful for determining quality of 
                           anomalous data for a MAD experiment. Thanks to
                           Tom Terwilliger for suggesting this.)
    xtal_patterson/patterson_map.inp (set default resolution to be 15A to 4A)
                   predict_patterson.inp ( " )
                   patterson_refine.inp  ( " )
    xtal_mmcif/deposit_mmcif.inp (default is to deposit unmodified experimental
                                  data, i.e. uncorrected for anisotropy)

- new files:
    general/rms_fit.inp (calculate and apply RMS fit between 2 molecules)

Modules:

- fixed major bugs in:
    xtal/scalenbulk (incorrect anisotropic scaling of intensities for the
                     MLI target)

- fixed minor bugs in:
    xtal/twin_operators (incorrect twin operator definition for point group 23)

- changes in:
    xtal/siterefine
    xtal/printcoordinates (correct printing of f'/f'' values by mad_phase.inp
                           summary file)

Libraries:

- added toppar/single_atoms.top and toppar/single_atoms.par to provide
  topology and parameters for isolated carbon and oxygen atoms. These can
  be used as scatterers when topology information is missing (e.g. when
  using an EM mask for molecular replacement).

Utilities:

- none

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