cctbx multi-platform build 2004_08_05

Build tag: 2004_08_05_0113

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] 12.8 MB
Mac OS 10.3.9 [Notes]	Python 2.3 ships with OS	[stream][direct] 14.4 MB
Red Hat 8.0	Python 2.2.1 ships with OS	[stream][direct] 7.9 MB
Red Hat 8.0 Python 2.3.4	[stream][direct] 19.0 MB	[stream][direct] 7.9 MB
Red Hat 9.0	Python 2.2.2 ships with OS	[stream][direct] 7.9 MB
Red Hat 9.0 Python 2.3.4	[stream][direct] 18.7 MB	[stream][direct] 7.9 MB
Red Hat WS 3	Python 2.2.3 ships with OS	[stream][direct] 7.9 MB
Windows 2000/XP Python 2.2.3	A bundle with a more recent Python is available	[stream][direct] 5.5 MB
Windows 2000/XP Python 2.3.4	[stream][direct] 8.7 MB	[stream][direct] 5.5 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

cctbx.geometry_restraints:
  - Improved and consolidated version of previous cctbx.restraints
    module which is now removed.
  - cctbx.crystal.minimization
    -> cctbx.geometry_restraints.energies, cctbx.geometry_restraints.lbfgs
  - cctbx.crystal.distance_ls
    -> cctbx.geometry_restraints.distance_least_squares

New cctbx.crystal.coordination_sequences module
  - based on code from early distance_ls.py

iotbx.pdb:
  - parser: processing of LINK records
  - New remark_290_interpretation
  - New format_scale_records() function based on code by Erik McKee

iotbx.lattice_symmetry:
  - reorganized so printout is separate function call

ccp4io:
  - fix for memory leak in cmtz library (fix provided by CCP4)

cctbx.xray.structure:
  - replace_scatterers() preserves existing site_symmetry_table by default

New cctbx.xray.minimization_add_restraints_site_gradients

New cctbx.crystal.correct_special_position() (fragment from
cctbx.restraints.lbfgs.apply_shifts)

cctbx.xray.structure:
  - change_basis(), expand_to_p1() enhanced to also work for
    anisotropic displacement parameters and moved to C++

Latest Boost CVS (2004_08_03_0137)
Latest CCP4 I/O CVS (2004_07_30_0213)
Latest SCons CVS (2004_08_03_0130)