CCI Apps bundles | Version 2008_09_13_0905 |
A password is required for all downloads. To obtain the password fill out this form.
Please do NOT install CCI Apps inside an existing Phenix
installation. It is best to install the CCI Apps bundle in a new,
separate, empty directory.
Order all source phenix_env and source cci_apps_build/setpaths
commands in chronological order (release date), oldest first,
most recent last.
(Use phenix.version to obtain the phenix release date.)
| Platform | Bundle |
|---|---|
|
Fedora Core 3 Python 2.5.2 | [stream] 55.1 MB |
|
Fedora Core 3 (x86_64) Python 2.5.2 | [stream] 55.9 MB |
|
Fedora Core 4 Python 2.5.2 | [stream] 55.9 MB |
|
Fedora Core 6 Python 2.5.2 | [stream] 55.9 MB |
|
Fedora Core 6 (x86_64) Python 2.5.2 | [stream] 57.1 MB |
|
Fedora Core 8 (x86_64) Python 2.5.2 | [stream] 56.3 MB |
|
Fedora Core 9 (x86_64) Python 2.5.2 | [stream] 55.6 MB |
|
Mac OS 10.4.10 (i386) [Notes] Python 2.5.2 | [stream] 54.4 MB |
|
Mac OS 10.4.10 [Notes] Python 2.5.2 | [stream] 54.9 MB |
|
Red Hat 8.0 Python 2.5.2 | [stream] 56.9 MB |
|
Red Hat WS 3 Python 2.5.2 | [stream] 53.9 MB |
|
Red Hat WS 3 (x86_64) Python 2.5.2 | [stream] 55.3 MB |
|
SuSE 9.2 (x86_64) Python 2.5.2 | [stream] 57.9 MB |
|
Compaq Tru64 V5.1 cxx V6.5-042 Python 2.5.2 | [stream] 71.4 MB |
|
Windows 2000/XP Visual C++ 7.1 Python 2.5.2 | [stream] 52.1 MB |
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 cci_apps_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.
source /usr/local/cci_apps_2007_03_26_1903/cci_apps_build/setpaths.csh
source /usr/local/cci_apps_2007_04_06_1210/cci_apps_build/setpaths.csh
To use a specific version of a command enter, e.g.:
phenix.refine_2007_03_26_1903
or
phenix.refine_2007_04_06_1213
Note that tcsh and bash support easy access to the alternative versions,
e.g. in tcsh
phenix.refine<Ctrl-D>
will list the two alternatives above. In bash the same can be achieved
by hitting the Tab key twice:
phenix.refine<Tab><Tab>
perl cci_apps_python_252_bundle.selfx
This installs Python 2.5.2 and all CCI Apps 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 cci_apps_python_252_bundle.selfx 4
Alternative for manual installation:
cci_apps_python_252_bundle.tar.gz
[stream]
47.2 MB
The
cctbx installation instructions
apply. The only difference is to specify phenix
instead of mmtbx when running the
libtbx/configure.py command.
2008_09_13_0905
Maintenance release:
- phenix.xtriage:
- bug in measurability interpretation fixed
- scoring function in point group determination now actively uses
estimated standard deviations
- when higher metric symmetry is possible, data is merged in highest
metric symmetry and possible spacegroups are suggested
2008_08_09_0053
Parallel release: Phenix 1.3 final
2008_07_25_1259
Parallel release: Phenix 1.3 rc4
2008_05_25_1144
Parallel release: Phenix 1.3 rc2
- phenix.refine:
- new refinement.geometry_restraints.edits.bond.slack parameter
- new show_histogram_slots, show_max_lines parameters
- new RNA sugar pucker analysis, specific restraints for
2' and 3' conformations (this is the default but can be
disabled rna_sugar_pucker_analysis.use=False)
- PDB output: write "H" space group symbols for rhomohedric space
groups using hexagonal basis (e.g. "H 3" or "H 3 2")
- new phenix.model_vs_data command: quick model vs. data statistics
(e.g. R-factors and bulk-solvent parameters)
- phenix.reduce now works under Windows
2008_05_03_2330
Maintenance release:
- phenix.refine: apply_cif_link fixes, addition of water hydrogen fixes
- new example: iotbx/iotbx/example/mtz_free_flipper.py
2008_04_25_1421
phenix.refine:
- proper automatic group occupancy refinement selections
- bug fix: crash when twin refinement is done in combination
with water picking
- new feature: automatic building of water hydrogen atoms based
on mFo-DFc maps (for sub-atomic resolutions)
- "stir" functionality re-worked (incrementally add high-resolution
reflections in refinement)
- water picking enhancements:
- always refine just water ADP when adding waters
- option to refine just water occupancies (when adding water)
- option to refine isotropic or anisotropic water ADP
(useful at ~1.2A and higher)
- evaluate secondary map cutoff for waters at exact oxygen
positions
- automatically detect waters drifted away too far from
the original sites and shift back
- default secondary map cutoff increased from 1.0 to 1.5 A
- joint x-ray/neutron refinement:
- bug fix: use both datasets in occupancy refinement
- assert common reflections to be used as test flags for both
datasets (generate if not provided); new option to ignore it
- smarter interpretation of SEGID column (atoms added with COOT
don't inherit the SEGID of atoms in the same residue or chain)
phenix.elbow:
- improved covalent bonding features
- convergence of AM1 optimization greatly improved
new phenix.ready_set:
- adds hydrogens to protein and ligands
- generates restraints files using the monomer library and
"chemical components" information from the PDB (this adds
about 25 MB to the download size)
phenix.pdbtools:
- support for user-supplied monomer library style cif files
(similar to phenix.refine)
phenix.pdb.hierarchy:
- completely reworked
- comprehensive PDB error and warning messages
- option to write out crystallographic and coordinate sections
complete with all TER cards
Version 2008_02_08_1610
phenix.refine:
- all incomplete monomer library files removed (about 2000 removed)
- electron density map parameters redesigned to support calculation
of maps with arbitrary F-obs, F-calc factors
- automatic NCS detection: always exclude H and D atoms from NCS
- NCS restrains: proper handling of alternative conformations
- geometry minimization of hydrogen atoms if riding model is used;
in the previous version some geometry distortions were ignored
- IAS refinement: reduced memory requirements (default map grid size
reduced)
- bug fix in IAS refinement: crash if used in restrained refinement
- phenix.refine manual: guidelines for high resolution refinement added
- phenix.refine QuickFacts updated
phenix.elbow:
- added all group III-VII elements up to Xe into AM1 method
including Boron and Selenium
phenix.pdbtools:
- support "occupancy.set=VALUE" for any selected part of a model
- phenix.geometry_minimization integrated into phenix.pdbtools
Version 2008_01_09_2058
phenix.refine:
- bug fix in wxc and wxu weights optimization (optimize_wxc and
optimize_wxu keywords)
- allow to switch between iso/aniso ADP for newly added solvent
(ordered_solvent.new_solvent = *isotropic anisotropic)
- allow to refine individual occupancies for newly added solvent
(without re-running phenix.refine, refine_occupancies key)
- always refine ADP for solvent at the moment of placing it (avoid
divergent refinement at resolutions approx. <1.5A)
- H-bond selection criterion added for water picking (default:
use_h_bond_rejection_criteria = True)
- constraints for occupancy refinement for atoms in alternative
conformations (sum of partial occupancies = 1)
- smart occupancy refinement handling: by default, phenix.refine always
refines occupancies for atoms in alternative conformations and those
having partial occupancies
- hydrogens in refinement: option to turn on/off contribution of H atoms
to scattering (contribute_to_f_calc), new keyword "refine_occupancies =
one_q_per_residue *one_q_per_molecule individual"; overall cumulative
improvements of handling H in refinement
- report list of highest peaks and deepest holes in difference map after
refinement (end of .log file)
- new experimental refinement.simulated_annealing.interleaved_minimization
option
- name change: dbe is gone entirely and ias is used everywhere instead
phenix.superpose_pdbs:
- bug fix
Version 2007_11_18_2203
Exact subset of phenix-1.3b-rc6
Version 2007_08_18_1856
phenix.reduce updated to produce PDB-V3 hydrogen names (Duke group)
phenix.refine updated to handle the new atom names from the remediated
PDB-V3. Currently protein and RNA/DNA only. For ligands with new names,
use elbow.builder to generate CIF files with matching restraints.
phenix.refine now writes a PDB deposition header
phenix.refine manual significantly re-worked
phenix.refine bug fixes:
- Proper handling of chain breaks, to avoid incorrect angle,
dihedral, chirality and planarity restraints. This bug
was likely to lead to bad restraints for structures with
alternative conformations.
- Avoid Wilson B crash for no data if low resolution omitted
- Proper handling of NCS + remove_h=true
- Proper handling of negative residue numbers
- Avoid segfault in twin refinement
- Cumulative fixes and enhancements in picking and refinement of
interatomic scatterers (IAS)
phenix.refine vdw_1_4_factor changed from 2/3 to 0.8 (to improve
geometry and MolProbity clash scores in particular)
phenix.refine obsolete remove_hydrogens option removed
New phenix.pdbtools (use --help)
Command aliases removed (i.e. mmtbx.xtriage is now only available
as phenix.xtriage)
Most major commands renamed to phenix.*, e.g.
iotbx.emma -> phenix.emma
iotbx.pdb.hierarchy -> phenix.pdb.hierarchy
Use phenix (in most shells) to get a full list of available
phenix commands.
eLBOW
- Perform simple eLBOW jobs in COOT
- Automatically perform the appropriate calculations on all the unknown
ligands in a PDB file and combine the CIF results into one file
- Covalent bonding of ligands to macromolecules (phase I implementation)
- Print the sequence of PDB file (elbow.print_sequence)
- User control of addition and writing of Hydrogens
- Output of TRIPOS mol2 files
- User control over naming of output files
- elbow.join_cif_files has re-ordered arguments (target as last argument)
- elbow.link_edits will generate "edits" from PDB LINK records for input
to phenix.refine
- elbow.metal_coordination will generate phenix.refine "edits"
for metal coordination spheres including angles
Version 2007_05_29_2026
Bug fix: twin refinement (wrong weight for X-ray/ADP term => refinement
unstable)
Site symmetry enforced for ADP shaking (weight calculation) in
anisotropic ADP refinement (no more eventual crashes due to
corresponding assertion error)
Bug fix: anisotropic ADP refinement for a model with hydrogens
(ridding refinement of H)
Bug fix: inconsistency in group B refinement due to
deep_copy method problem in twin_f_model.py
Various subject added to phenix.refine documentation (using
phenix.refine to calculate a model map calculation, ignoring
free-R flags in refinement)
Difference map based IAS picking (for ultra-high resolution
refinement, higher than 0.9A)
CNS 1.2 compatibility for ATOM records with
serial numbers > 99999
Various minor enhancements and bugs fixes
Version 2007_04_26_2350
Maintenance release (bug fixes)
Version 2007_04_06_1210
phenix.refine: new support for custom angle restraints;
determination of nonbonded distances distinguishes between refinement
with and without hydrogens (based on remove_hydrogens=True/False).
Version 2007_04_04_2342
*** RETRACTED BECAUSE OF BUG ***
Version 2007_03_26_1903
Integration of the reduce program into CCI Apps (phenix.reduce).
phenix.refine documentation updated.
Final f_model exported as proper MTZ or CNS file (was ad-hoc before).
Some bug fixes.
Version 2007_03_13_2155
Mainly accumlated bug fixes.
New features (not fully completed/documented): group_anomalous
refinement, twin refinement (least-squares target), support for
refinement with all hydrogens.
Version 2007_01_24_2154
Simultaneous use of NCS restraints and automatic water picking.
Individual anisotropic ADP restraints (similar to SHELXL SIMU).
Bug fix in processing of multiple apply_cif_link blocks applied
to the same residue.
Version 2007_01_11_0918
apply_cif_modification, apply_cif_link, binning fixes,
individual occupancy refinement, group occupancy refinement,
automatic NCS detection
Version 2006_11_01_1257
Mainly bug fixes. phenix.refine supports more combinations of water
picking and various refinement strategies (but not NCS yet, sorry).
Version 2006_10_19_2227
Reorganized phenix.refine parameters
Version 2006_10_02_2327
Latest twinning tools for Phenix consortium members
NOTE: the phenix.refine documentation is not up to date!
Version 2006_07_05_2228
Subset of phenix release 1.24.1b (2006 Jul 05)
Version 2006_05_16_1726
Latest elbow.builder for Phenix consortium members
Version 2006_05_01_1334
Latest elbow.builder for Phenix consortium members
Version 2006_04_19_1411
Bug fix in phenix.refine rigid-body refinement ("scrambled eggs")
Version 2006_04_08_2139
First public release, includes elbow
Version 2006_02_27_2221
Paul's trip to Barcelona
Version 2005_12_29_2029
Support Sacha's workshop
Version 2005_12_18_1014
First complete multi-platform build as cci_apps