cctbx multi-platform build 2005_01_22

Build tag: 2005_01_22_0855

Self-extracting binary distributions

cctbx+Python bundles are larger but completely self-contained.
cctbx only bundles use the Python that ships with the OS or require that a matching Python version is installed separately.
Use [stream] if your browser displays the [direct] download in a text window instead of saving it to a file.
Use cctbx.python to run scripts. The plain python command is not longer supported to avoid confusion with the Python version provided by some operating systems.

Platform	cctbx+Python	cctbx only
IRIX 6.5.10 MIPSpro 7.3.1.2 Python 2.4	[stream][direct] 27.5 MB	[stream][direct] 18.4 MB
IRIX 6.5.21 MIPSpro 7.41 Python 2.4	[stream][direct] 26.9 MB	[stream][direct] 18.0 MB
Mac OS 10.2.8 [Notes] Python 2.3	Python 2.3 must be installed separately	[stream][direct] 14.1 MB
Mac OS 10.3.9 [Notes]	Python 2.3 ships with OS	[stream][direct] 15.7 MB
Red Hat 7.3 Python 2.4	[stream][direct] 25.9 MB	[stream][direct] 14.1 MB
Red Hat 8.0	Python 2.2.1 ships with OS	[stream][direct] 8.9 MB
Red Hat 8.0 Python 2.4	[stream][direct] 21.6 MB	[stream][direct] 8.9 MB
Red Hat 9.0	Python 2.2.2 ships with OS	[stream][direct] 8.9 MB
Red Hat 9.0 Python 2.4	[stream][direct] 21.4 MB	[stream][direct] 8.9 MB
Red Hat WS 3	Python 2.2.3 ships with OS	[stream][direct] 8.9 MB
Red Hat WS 3 Python 2.4	[stream][direct] 19.0 MB	[stream][direct] 9.0 MB
Compaq Tru64 V5.1 cxx V6.5-042 Python 2.4	[stream][direct] 24.9 MB	[stream][direct] 16.6 MB
Windows 2000/XP Python 2.2.3	A bundle with a more recent Python is available	[stream][direct] 6.1 MB
Windows 2000/XP Python 2.4	[stream][direct] 10.0 MB	[stream][direct] 6.1 MB

[Other platforms]

Download the self-extracting binary distribution for your platform to any new, empty directory. Under Unix selfx bundles are installed with the perl command (which is available by default on all supported platforms), for example:

    perl cctbx_redhat80.selfx

Under Windows exe distributions are installed simply by running them.

The installer must be run on the platform where it is used. The installed package may be used over the network, but only if the pathnames to the installation directory are identical on the server and the client.

Uninstalling a bundle is as easy as using rm -rf * in the installation directory under Unix or dragging the installation directory to the Recycle Bin under Windows. The Windows registry is not modified by the installation.

[Installation overview]

Self-extracting cctbx and Python 2.4 sources for Unix

cctbx_python_24_bundle.selfx [stream][direct]
23.7 MB

Download the file and run the following command in any new, empty directory:

    perl cctbx_python_24_bundle.selfx

This installs Python 2.4 and all cctbx modules from scratch.

The install script will prompt for the number of available CPUs. To avoid the prompt (e.g. for scripting the installation), add the number of available CPUs to the command line. E.g.:

    perl cctbx_python_24_bundle.selfx 4

Alternative for manual installation:
cctbx_python_24_bundle.tar.gz [stream][direct]
23.7 MB
[Installation instructions]

Self-extracting cctbx sources for Unix

cctbx_bundle.selfx [stream][direct]
14.8 MB

Download the file and run the following command in any new, empty directory:

    perl cctbx_bundle.selfx

This installs all cctbx modules from scratch. Python 2.2.1 or higher must be pre-installed on the target machine. Known to work under Redhat 8.0 or higher with the Python version that ships with the operating system (/usr/bin/python). The first python on PATH is used. To install with a different, specific python, add the full path to the command line, e.g.:

    perl cctbx_bundle.selfx /usr/local/bin/python

Alternative for manual installation:
cctbx_bundle.tar.gz [stream][direct]
14.8 MB
[Installation instructions]

Self-extracting cctbx sources for Windows

cctbx_bundle.exe [stream][direct]
21.8 MB

Execute this file in any new, empty directory to unpack the sources required for compiling all cctbx modules from scratch.
[Installation instructions]

Changes

mmtbx:
  - http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/

PyCifRW integration:
  - http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/

iotbx.reflection_statistics:
  - show possible twin laws
  - show correlations for all possible reindexing choices
  - show patterson peaks
  - show perfect merohedral twinning test

iotbx.show_distances:
  - automatic detection and processing of PDB files
  - new --show_cartesian option

iotbx.pdb.interpretation.stage_1.extract_xray_structure():
  - label=atom.pdb_format()
  - new infer_scattering_types_from_names option
  - new unknown_scattering_type_substitute option

iotbx.pdb.atom.selection_cache:
  - new selection() and iselection() methods operating on
    expressions such as "rename ala and (name ca or name n)"

new iotbx.simple_parser
  - to support atom selection syntax

iotbx.mtz reworked

cctbx.xray.structure:
  - scattering_dict(): optional types_without_a_scattering_contribution
    parameter
  - new pair_asu_table() and show_pairs() convenience methods
  - new set_u_iso_from_u_star()

cctbx.miller:
  - new set.as_non_anomalous_set()
  - new array.as_non_anomalous_array()
  - new array.average_bijvoet_mates()
  - array.change_basis() now supports all array types (phases,
    complex, hendrickson_lattman)
  - new set.customized_copy()
  - new array.customized_copy()
  - set.common_set() and miller.set.common_sets() changed:
      a.common_set(b) now returns a set (or array) with the indices
      ordered as in b, instead of as in a as before;
      for consistency, a,b = a.common_sets(b) also returns indices
      ordered as in b.
  - binner reworked to support nicer output
      as a side-effect array.show_completeness_in_bins()
      is obsolete and was removed.

cctbx.crystal:
  - new asu_clusters algorithm
  - new crystal.reindexing_info class
  - new crystal.symmetry.reindexing_info() method
  - new crystal.symmetry.reindexing_matrices() method
  - new crystal.symmetry.customized_copy()
  - neighbors_simple, neighbors_fast: new neighbors_of() method

cctbx.sgtbx:
  - new cosets module
  - new space_group.build_derived_reflection_intensity_group()
  - new space_group.build_derived_acentric_group()
  - new rot_mx.transpose()
  - new rot_mx.as_xyz()
  - new rot_mx.as_hkl()
  - new change_of_basis_op.as_xzy()
  - new change_of_basis_op.as_hkl()
  - rt_mx and change_of_basis_op constructors accept h,k,l strings

cctbx.uctbx.unit_cell:
  - new similarity_transformations() method
  - modified constructors:
      parameters=...
      metrical_matrix=...
      orthogonalization_matrix=...

new cctbx.crystal.burzlaff_zimmermann_dewolff
  - demonstration of the practical problems associated with
    the use of character tables for the determination of the
    lattice symmetry (by N.K. Sauter)

new cctbx.adp_restraints (by P.V. Afonine)

scitbx.array_family.flex.double:
  - new matrix methods:
      matrix_diagonal
      matrix_diagonal_sum, matrix_trace
      matrix_diagonal_product
      matrix_multiply, dot
      matrix_lu_decomposition_in_place
      matrix_lu_back_substitution

scitbx.lbfgs:
  - all parameters for drop_convergence_test included in
    termination_parameters
  - objective function value at starting point is now passed to
    drop_convergence_test

ccp4io:
  - cmtz library is now a shared library on most platforms

libtbx:
  - new libtbx.phil: Python-based hierarchical interchange language
      http://iucrcomputing.ccp14.ac.uk/iucr-top/comm/ccom/newsletters/2005jan/
  - new libtbx.introspection
  - new support for defining paths to sources via files (instead of softlinks)

Transition to Python 2.4 (but Python 2.2 and 2.3 are still supported)

Latest Boost CVS (2005_01_21_1616)
Latest CCP4 I/O CVS (2004_11_12_0839)
Latest SCons CVS (2005_01_21_1609)
Latest Clipper (2004_11_01)