cctbx multi-platform build 2004_07_06

Build tag: 2004_07_06_0816

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
Mac OS 10.2.8 [Notes] Python 2.3	Python 2.3 must be installed separately	[stream][direct] 12.6 MB
Mac OS 10.3.9 [Notes]	Python 2.3 ships with OS	[stream][direct] 14.2 MB
Red Hat 8.0	Python 2.2.1 ships with OS	[stream][direct] 7.7 MB
Red Hat 8.0 Python 2.3.4	[stream][direct] 18.9 MB	[stream][direct] 7.7 MB
Red Hat 9.0	Python 2.2.2 ships with OS	[stream][direct] 7.7 MB
Red Hat 9.0 Python 2.3.4	[stream][direct] 18.5 MB	[stream][direct] 7.7 MB
Red Hat WS 3	Python 2.2.3 ships with OS	[stream][direct] 7.7 MB
Windows 2000/XP Python 2.2.3	A bundle with a more recent Python is available	[stream][direct] 5.4 MB
Windows 2000/XP Python 2.3.4	[stream][direct] 8.6 MB	[stream][direct] 5.4 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 2.3.4 sources for Unix

cctbx_python_234_bundle.selfx [stream][direct]
21.2 MB

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

    perl cctbx_python_234_bundle.selfx

This installs Python 2.3.4 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_234_bundle.selfx 4

Alternative for manual installation:
cctbx_python_234_bundle.tar.gz [stream][direct]
21.2 MB
[Installation instructions]

Self-extracting cctbx sources for Unix

cctbx_bundle.selfx [stream][direct]
13.0 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]
13.0 MB
[Installation instructions]

Changes

Integration of Kevin Cowtan's Clipper libraries.

mmtbx:

  - Automatic X-ray term weight calculation procedure improved by
    introducing the model regularization (minimization of geometry
    term only) prior to the dynamics calculation.

  - Bulk solvent correction and scaling procedure significantly improved:
    flat bulk solvent model parameters, ksol and bsol, are now
    determined via a grid search (minimizing the R-factor) instead of
    using the minimizer.

  - Full maximum-likelihood target function with two ways
    of calculating the distribution parameters (alpha and beta):
      a) alpha & beta estimated by maximization of the likelihood
         function given a current model and experimental intensities.
      b) alpha = 1.0 & beta - calculated by exact formula.

  - Calculation of a priori probability distribution for ordered
    solvent.

  - Presentation of intermediate results during refinement significantly
    improved.

  - Python code for restrained Cartesian dynamics moved from Python to C++.

  - Automatic detection of R-free flags in CNS, SHELX and CCP4
    formatted hkl files.

cctbx::sgtbx::site_symmetry
  - derived from new site_symmetry_ops to facilitate tabulation of only
    the essential data (site_symmetry_ops::special_op,
    site_symmetry_ops::matrices)
  - bug fix: uninitialized data member when used in connection with
    wyckoff::table
  - Python keyword argument support

new cctbx::sgtbx::site_symmetry_table

cctbx::crystal::direct_space_asu::asu_mappings:
  - Integration of cctbx::sgtbx::site_symmetry_table
  - min_distance_sym_equiv member removed
  - process variants with site_symmetry_ops/table as parameters

cctbx::sgtbx::sym_equiv_sites:
  - Constructor with site_symmetry_ops parameter

Pickle support for cctbx.sgtbx.rt_mx, cctbx.sgtbx.site_symmetry_ops, and
cctbx.sgtbx.site_symmetry_table

cctbx.crystal.symmetry:
  - new asu_mappings()
  - niggli_cell() with relative_epsilon, iteration_limit parameters

cctbx.xray.scatterer:
  - apply_symmetry_site(), apply_symmetry_u_star() with site_symmetry_ops
    as parameter
  - Obsolete update_weight() method removed

cctbx.xray.structure:
  - Integration of cctbx.sgtbx.site_symmetry_table
  - apply_symmetry() overload with site_symmetry_ops as parameter
  - new apply_symmetry_sites()
  - new n_undefined_multiplicities()
  - new set_sites_frac(), set_sites_cart()
  - rms() -> rms_difference()

cctbx.crystal.distance_ls completely overhauled

iotbx.kriber.strudat:
  read_entry.connectivities(self, all_or_nothing=00000)

New iotbx.show_distances, iotbx.distance_least_squares

New scitbx.stl.map, scitbx.stl.set scitbx.stl.vector modules

Python slice wrapper moved to new scitbx.boost_python.slice extension

libtbx.configure now adds packages unless the new --only option is used
new libtbx.configure --help option

Work in progress: geometry restraints reorganized
  - new bond_sym_table, bond_sym_dict, bond_sym_ops, bond_sym_op
  - bond_asu_proxy, repulsion_asu_proxy: inherit from asu_mapping_index_pair
  - new bond_params: base class for bond_simple_proxy, bond_asu_proxy, bond
  - bond_proxy -> bond_simple_proxy
  - repulsion_proxy -> repulsion_simple_proxy
  - sorted_proxies -> sorted_asu_proxies

Latest Boost CVS (2004_07_05_2138)
Latest CCP4 I/O CVS (2004_07_03_0431)
Latest SCons CVS (2004_07_06_0802)