CHANGE LOG for PHENIX distribution
		==================================

Version 1.3
===========

- General:
  - Release version 2008
  - Changes to installer to check for csh/tcsh
  - changes in svn_checkout command
  - incorporated the PDB chemical components dictionary to aid with the
    interpretation and processing of ligands
  - infrastructure for OpenMP compilation added

- Wizards:
  - AutoSol:
    - Scoring now uses Bayesian estimation of correlation coefficient
    - Building changed to helices and stands by default (faster)
    - Building will continue with more thorough algorithm if it
      fails to build with the fast algorithm
    - When testing both hands in building the best model from the first
      hand will not be overwritten with the current model from the
      second hand unless it is better
  - AutoBuild:
    - Parallelized for running on SMP architectures using threads

- phenix.refine
  - complete rewrite of PDB handling - new model hierarchy, faster structure 
    reading, and direct structure writing. 
  - constrained group occupancy refinement applied to alternate conformations
    by default
  - algorithms implemented for hydrogen and deuterium picking in neutron/X-ray
    maps
  - numerous changes to better handle joint refinement of X-ray/neutron data
  - map coefficients written for an anomalous difference Fourier map if anomalous 
    data is used

- phenix.xtriage
  - analysis of systematic absences

- phenix.elbow
  - extended to more element types
  - bug fix to deal with close atoms recognized as bonds
  - Numeric SVD code used for larger structures (addresses bug in tntbx)

- phenix.reel
  - more model manipulation features added

- Phaser:
  - minor bug fixes

- phenix.reduce
  - minor bug fixes

Version 1.3b
============

- General:
  - support for 2 letter chain IDs.
  - support for Hybrid36 atom and residue numbers.
  - Mac OSX port (PowerPC and Intel)
  - GUI modifications to support the Mac
  - Conversion to latest wxPython (2.8.4.0) and associated libraries
  - Installer modifications to support Mac-OSX port
  - Removed C++ library test on linux platforms
  - New tools: phenix.xmanip, phenix.pdbtools, phenix.reel, 
               phenix.find_helices_strands, 
  - New document generation system
  - Full documentation

- Wizards:
  - Simple command-line versions of all Wizards
  - AutoBuild:
    - Automated nucleic acid model building
    - Simple-omit, sa-omit, and iterative-build-omit maps
    - Automatic treatment of ligands when rebuilding models
    - Simple commands for building multiple models compatible with data
    - Simple command for rebuilding to produce one very good model
    - Prime-and-switch maps
    - Iterative model-building of strands and helices at low resolution
  - AutoMR
    - now using Phaser-2.1.2:
    - Default packing criteria relaxed in AUTO_MR mode
    - Composition can be estimated from solvent content
    - Default composition corresponds to 50% solvent
    - If AUTO_MR search finds some, but not all, components, the partial 
      solution is output
  - AutoSol
    - SAD phasing starting from MR partial model using Phaser
  - Ligand identification
    - Improved ligand scoring and ranking algorithm.
    - Implemented additional analysis of ranking results
    - Improved task display options
    - Task now accepts user-provided ligand library

- phenix.find_helices_strands: 
  - rapid fitting of secondary structure to an electron density map

- phenix.probe
  - better support for alternate names.
  - numerous bug fixes.

- phenix.reduce
  - updated het dictionary.
  - numerous bug fixes.

- 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.
  - Writing of a PDB deposition header
  - Constraints for occupancy refinement added (used in refinement of atoms 
    in alternative conformations);
  - Default behavior change: now phenix.refine always refines occupancies
    for atoms in alternative conformations or for atoms with partial 
    occupancies;
  - Water picking procedure improved: bug fix to remove waters located too 
    far from the molecule, H-bond criteria added;
  - Significant improvement in handling of hydrogens in refinement;
  - Bulk-solvent and scaling procedure made even more robust (B_cart 
    optimization is done a few times in-between grid search steps in 
    ksol and Bsol);
  - Documentationa reworked
  - Vdw_1_4_factor changed from 2/3 to 0.8 (to improve
    geometry and MolProbity clash scores in particular)
  - Obsolete remove_hydrogens option removed
  - Site symmetry enforced for ADP shaking (weight calculation) in 
    anisotropic ADP refinement (no more eventual crashes due to corresponding
    assertion error)
  - Complete set of tools for refinement at ultra-high resolution (higher 
    than 0.9A; modeling of bond electron density with interatomic scatterers,
    IAS)
  - New support for custom angle restraints
  - Determination of nonbonded distances distinguishes between refinement
    with and without hydrogens (based on remove_hydrogens=True/False);
  - Numerous enhancements for joint Xray+Neutron refinement (clearer handling
    of input data files, better targets weight calculation protocol)
  - MZ (multiple zone) rigid body refinement protocol is further optimized to 
    decrease the runtime, accommodate a provision for multiple refinable 
    rigid bodies.
  - A set of examples is added.
  - 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 negative residue numbers
    - Avoid "Segmentation fault" on Macs in twin refinement
    - Twin refinement (fix for wrong weight for X-ray/ADP term => refinement
      unstable)
    - Anisotropic ADP refinement for a model with hydrogens
      (riding refinement of H)
    - Fix inconsistency in group B refinement due to deep_copy method
      problem in twin_f_model.py

- phenix.pdbtools (new command-line tool for performing various manipulations
  on a model in a PDB file and general model statistics):
  - shaking of coordinates (random coordinate shifts)
  - rotation-translation shift of coordinates
  - shaking of occupancies
  - shaking of ADP
  - shifting of ADP (addition of a constant value)
  - scaling of ADP (multiplication by a constant value)
  - setting ADP to a given value
  - conversion to isotropic ADP
  - conversion to anisotropic ADP
  - removal of selected parts of a model
  - generates complete statistics for model geometry and Atomic Displacement
    Parameters.
  - tools for structure factors calculation from PDB model.
  - A documentation page added.

- phenix.cif_as_mtz (tool for conversion of reflection files in CIF format 
  into MTZ format). Main features include:
  - distinguishes between Iobs and Fobs;
  - distinguishes between Xray and Neutron data sets;
  - analysis and picks up valid R-free flags;
  - simple sanity check of data.
  - A documentation page added.

- phenix.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
  - improved chiral centre handling
  - access to all MSDChem SMILES strings
  - converted to PDBv3.0

- phenix.reel
  - alpha release of restraints editor
  - read, edit, optimise and write CIF files
  - run eLBOW from a GUI window

- phenix.xtriage
  - now handles unmerged data

Version 1.26.1b
===============

- Conversion to latest wxPython (2.8.1.1) and associated libraries
- Withdrawn support for SGI-Irix and Alpha-Tru64 (GUI libraries are 
  no longer supportable on these platforms)

Version 1.26b
=============

- General
  - Reduce (from Jane and Dave Richardson, Duke University) integrated into 
    PHENIX, available as phenix.reduce

- Wizards:
  - improved model building in AutoSol
  - improved model building in AutoBuild
  - Automated detection and application of NCS
  - Automated loop building, crossovers between chains in different models 
    of a structure, and side-chain optimization
  - SA-composite omit maps
  - Simple omit maps
  - Iterative-build composite omit maps
  - Omit around atoms in PDB file
  - Model rebuilding in place 

- Phaser:
  - Updated to version 2.1
  - Molecular replacement changes:
    - Clash test is more forgiving
    - Partial solution is output if full solution fails
  - SAD phasing includes partial structure option to start from molecular 
    replacement solution

- Textal:
  - Minor bug fixes

- Resolve ligand identification:
  - Improved ligand ranking algorithm 

- phenix.xtriage:
  - If pseudo translation peaks implicate a higher symmetry and/or smaller 
    unit cell, the appropriate unit cell and spacegroup are listed.
  - Optional detwining and treatment of data, including protocols for 
    anisotropy correction, outliers detection and twinning or detwinning 
    of data
  - xtriage code reorganized in such a way that it can be easily used in other
    scripts and the wizards  

- phenix.refine:
  - Bug fixes (major and minor)
  - Testing and bug fixes in TLS refinement
  - Final f_model exported as proper MTZ or CNS file (was ad-hoc before)
  - Group_anomalous refinement (for anomalous atoms such as Se)
  - Refinment of hemihedrally twinned data using a lsq target function
  - Output of 'detwinned' and gradient maps for twinned data
  - Support for refinement with hydrogens (not fully tested)
  - Simultaneous use of NCS restraints and automatic water picking
  - Individual anisotropic ADP restraints (similar to the SIMU restraint in 
    SHELX)
  - Flexible model parameterization (refinement can use rigid body, isoADP,
    anisoADP, etc simultaneously)
  - Simultaneous refinement of structures against X-ray and neutron data
  - Bug fix in processing of multiple apply_cif_link blocks applied to the 
    same residue
  - Changes to allow user specified covalent bonds: apply_cif_modification, 
    apply_cif_link
  - Fixes to binning to deal with sparsely distributed free-R set (e.g. thin 
    shells)
  - Individual occupancy refinement
  - Group occupancy refinement
  - Automatic NCS detection
  - Reorganization of phenix.refine parameters

- 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
  - Added classes to monitor peptide linkages, nitrogen planarity and acid 
    groups to maintain geometry during coordinate calculations
  - Greatly improved molecule matching procedures
  - User control of addition and writing of Hydrogens
  - User control of bond cutoff for auto bonding
  - User control of number optimisation steps and convergence tolerance
  - Output of TRIPOS mol2 files
  - User control over naming of output files
  - User control of total memory usage 
  - More tests added
  - AM1 optimisation includes peptide linkage correction and more efficient 
    search procedures
  - elbow.join_cif_files has re-ordered arguments (target as last argument)

- phenix.explore_metric_symmetry:
  - Renamed from iotbx.ehms
  - Generation of point group graphs given a unit cell and space group 
    combination
  - Comparison of unit cells and their sublattices

- phenix.twin_map_utils:
  - Refinement of twin fractions and map parameters for all possible twin 
    laws given a fixed model and a given dataset

- mmtbx.remove_outliers
  - Outlier removal using Wilson or model based statistics

- PHENIX GUI:
  - Minor bug fixes
  
- Installer:
  - New solve/resolve CVS installation
  - Updates to libtbx package installation
  - Improved developer tools for updating PHENIX components (cvs_checkout,
    svn_checkout)
  - Backwards compatibility checks in phenix_env to detect an installation 
    from an earlier OS and use it if necessary

Version 1.25b
=============

- Minor bug fixes

Version 1.24b
=============

- Wizards:
  - LigandFit Wizard made more robust and tested against 9000 
    ligands in PDB
  - IterativeBuild and ModelBuild Wizards combined into single 
    AutoBuild Wizard
  - AutoBuild Wizard 
    - Introduced "rebuild_in_place" for rebuilding MR models
    - Full-omit map and multiple-model generation available
  - AutoMR Wizard
    - Automatic rebuilding of MR solutions using AutoBuild 
      rebuild_in_place
  - AutoSol Wizard decision-making improved using model completeness 
    as a quality measure
  - All Wizards can be fully run with scripts 
  - Sample scripts available for all Wizards with data in $PHENIX/examples

- Phaser:
  - Integrated with AutoMr Wizard
  - Sphericity restraint on overall anisotropy
  - Improved pruning of list of plausible solutions
  - Various bug fixes for unusual space groups and non-Linux architectures

- Textal:
  - created a single integrated command-line script: textal.build
    options: build backbone only (C-alpha chains)            [--capra_only]
             build complete model (backbone and side-chains) [default]
             build side-chains for user-supplied C-alpha's   [--input_model]
  - reads reflection files or XPLOR maps for building
    options for region of space to build:
      - runs FINDMOL to automatically create map centered over a contiguous,
        symmetry-unique molecular region using symmetry ops and clustering
      - build in ASU [--asu]
      - build in user-supplied XPLOR map [--input_map]
  - will do sequence alignment to improve amino acid identity if
    amino-acid sequence file is provided [--sequence]
  - user can provide coodinates of Selenium sites (if available) to potentially
    improve accuracy of sequence alignment by identifying methionine 
    residues [--se_sites]
  - now runs simulated annealing (phenix.refine) automatically as final
    step to estimate R-factor (as an indicator of model quality)
  - new unified Textal task/strategy in Phenix GUI
    - graphical front-end to textal.build script; same options, all on
      one dialog box

- eLBOW
  - Documentation available in installation and on-line
    - computer resources page
  - Uses bond length defaults from HF/6-31G(d,p) quantum calculations
  - Uses GDIIS to improve geometry optimisation convergence and DIIS in 
    quantum convergence
  - Restart mechanism begins from previous best geometry
  - Expert/Novice modes
  - Can use GAMESS for geometry optimisation
  - Provides estimates of the computer resources needed for a calculation
  - Provides suggestions upon completion of a run
  - eLBOW will extract a specified ligand from a PDB file containing both 
    protein and ligand
  - eLBOW will dynamically update geometry visualised in PyMOL
  - eLBOW can construct a short protein sequence
  - eLBOW can use a file as a template to name the ligand atoms
  - Database of SMILES and PDB files included
  - Input can be piped to eLBOW 

- iotbx.ehms:
  - Minor updates to functionality and output
  - Centring type is inputable rather than just a spacegroup 

- mmtbx.xtriage:
  - Maximum likelihood based estimation of twin fraction
  - Maximum likelihood based estimation of twin fraction 
    while taking into account possible NCS parallel to 
    the twin axis.
  - PHIL Interface rationalisation:
    - Detwinned data can be written out
    - various parameters can be set by the user if desired
  - Help/Manual updated (mmtbx.xtriage --h)
  - various bug fixes

- phenix.refine:
  - NCS restraints (coordinates and ADPs)
  - TLS refinement
    - Recalculation of TLS parameters from overall ADPs values
    - Parameter modification to remove positive definite atomic aniso-Us
    - TLS parameters written in output PDB file
    - Options:
      - TLS alone
      - TLS plus ADPs
      - TLS plus ADPs and coordinates
  - Group B-factor refinement
  - Rigid body refinement
  - Simple structure factor calculations (with or without bulk solvent 
    and scaling)
  - Output MTZ coefficients for use in COOT
  - Increased checking of input PDB files and reflection data
  - Updated documentation

- PHENIX GUI:
  - color indicators added to show when a strategy/wizard icon has been
    double-clicked
  - strategies and tasks rationalized
  - improved default map and coordinate viewing options when displaying
    results in PyMOL
  
- Installer:
  - updated to 0.99rc6 version of PyMol
  - updated to more recent versions of freetype, fontconfig and pango on linux.
    This fixes a memory allocation problem on Fedora Core 5.
  - added --alias_mtype option to installer to force installation of
    a different machine type (binaries only). May be necessary on some
    SuSE systems. 
  - now using freeglut and latest 8.4.x versions of tcl/tk
  - solve/resolve source code now included in the distribution
  - examples directory restructured and more examples/tests added

Version 1.23a
=============

- New tool: iotbx.ehms
  Explore Higher Metric Symmetry. Allows one to easely compute/list
  all possible point and spacegroups allowed by a certain point or
  spacegroup. A graph is constructed and is plotted if graphiv is
  installed.

- mmtbx.xtriage updates:
  - Data strength analysis
  - Low resolution completeness reporting
  - Wilson plot sanity analyses
  - Outlier detection based on Wilson statistics
  - Ice ring detection
  - Anomalous difference analyses
  - More elaborate reporting on type of twin laws
  - If calculated data is supplied next to experimental data,
    R.vs.R statistics is reported (Lebedev et al, Acta Cryst.
   (2006). D62, 83-95)
  - Missing rotational symmetry analyses. If symmetry is too low,
    new spacegroup is suggested on basis of R-value.
  - various bug fixes

- New tool: mmtbx.fest
  - Simple delta F and Fa construction from 2-lambda MAD, SAD SIR or RIP
    data.
  - Various scalings protocol can be chosen. Most (if not all)
    critical parameters can be set/modified by the user.

- New tool: eLBOW

Version 1.22a
=============

- Updated version of SOLVE/RESOLVE (2.11)
- Generation of environment file for sh/bash

Version 1.21a
=============

- Updated wizard infrastructure:
  - Wizards can call other wizards
  - Bug fixes and changes to AutoSol and AutoMR
  - New loop-fitting algorithm implemented in RESOLVE
  - New Iterative, TextalBuild and ResolveBuild Wizards
- New automatic ligand geometry and restraint building (ELBOW):
  - semi-empirical method for determination of coordinates
  - generation of coordinates from SMILES
  - generation of monomer library (cif) files for refinement 
- Updated phenix.refine:
  - improved performance (1.5 to 2 times faster)
  - automated water picking
  - local-neighborhood individual ADP restraints
  - improved bulk-solvent/anisotropic scaling calculations
  - new automated weight generation scheme
  - refinement against neutron diffraction data
- New data analysis tool: mmtbx.xtriage
  - automated detection of anisotropy, twinning, and 
    non-crystallographic translational symmetry
  - maximum likelihood determination of anisotropic and absolute
    scaling parameters
  - automatic determination of possible twin laws
- Infrastructure:
  - latest versions of thrid-party GUI libraries (glib, gtk+, 
    wxWidgets and wxPython)
  - removed BLT from installation
  - linux installation modified to account for new x86_64 architectures 
    and new linux 2.6 kernel
  - SGI installer

Version 1.2a
============

- Updated wizards

Version 1.1a
============

- Release version based on 1.08a
- Minor bug fixes for TEXTAL, SOLVE/RESOLVE strategies
- Minor bug fixes for PHENIX GUI
- Additional documentation - HySS and phenix.refine

Version 1.08a
=============

- Structure refinement (phenix.refine) including:
  - LBFGS minimization
  - Cartesian dynamics simulated annealing
  - Maximum likelihood with amplitudes
  - Maximum likelihood with amplitudes and phases
  - Restrained individual B-factor refinement
  - CCP4 monomer library for geometry restraints generation
  - Automatic input PDB interpretation
  - Automatic input data interpretation
- Latest version of PHASER (1.3)
  - Bug fixes from Phaser-1.2
  - Improved automated MR
  - Final phasing and refinement to full resolution
  - Improved packing
    - RNA/DNA
    - close-packed oligomers
    - only most homologous model in ensemble used for analysis
  - Reduced memory requirements
- Latest version of TEXTAL
  - Builds models from structure factors
    - users no longer required to prepare a centered density map
    - will automatically adjust resolution as necessary, and can
      now build models for datasets at 3.0A resolution or higher
  - Automated detection, centering, and tracing of protein molecules
    using the FINDMOL algorithm
  - Simplex optimized model building for better CA positions and side-chain
    identities
  - Task re-organization into hierarchical groups:
    - New high-level tasks to simplify model building
    - utilities and primitive tasks (for experts)
  - Invocation of many Textal routines from command line
- Wizards
  - Updated AutoSol and AutoBuild wizards
  - New AutoMR wizard for automated molecular replacement
  - New AutoLig wizard for automated ligand fitting
- Latest solve/resolve version - 2.09
- Updated solve/resolve strategies
- Infrastructure
  - PHENIX installation co-exists with other cctbx-based packages
  - PHENIX co-exists with Linux GNOME environment
  - Now using Python 2.4.1
  - Now using version 2.0+ of GTK+
  - Now using latest versions of wxGTK (wxWidgets) and wxPython
  - Now using PyMOL 0.97

Version 1.07a
=============

- Added Wizard infrastructure to PHENIX
- Wizards for automatic structure solution and model building
- Improved use of UNIX domain sockets
- Fixes in PHASER code for SGI and Alpha platforms
- Updated PHASER strategies
- Updated TEXTAL strategies
- New TEXTAL stitch algorithm for gap closure
- Updated SOLVE/RESOLVE strategies
- New strategies added for running phase improvement with RESOLVE
- Updates to the PHENIX GUI infrastructure
- Splash-page documentation added
- SOLVE/RESOLVE incorporated in the PHENIX distribution
- Test for appropriate version of make for source installation
- Fixes to glib configure script for Alpha
- Fixes to wxGTK configure and source code for Alpha
- Installer compiles Python with C++ compiler if required 
  for wxPython compilation
- RedHat 7.3 removed from supported platforms
- Additional command line options for HySS
- Improved the killing of strategies
- Added ability to run strategies in queuing systems
- Sun Grid Engine currently supported for queuing (this may work
  with other queuing systems, but is not tested)

Version 1.06a
=============

- Minor bug fixes in GUI
- Added option to use rsh instead of ssh to run remote jobs
- New detection of network status on startup
- Use UNIX domain sockets if network is not functioning
- Updated tasks and strategies for PHASER
- Improved map reading speed in TEXTAL tasks

Version 1.05a
=============

- New tasks and strategies for PHASER
- New tasks and strategies for TEXTAL
- New map database for TEXTAL
- Bitmaps for task and strategy canvas in PHENIX GUI

Version 1.04a
=============

- New tasks and strategies for SOLVE/RESOLVE
- Improvements to hostname resolution to deal with incorrectly 
  configured systems

Version 1.03a
=============

- New installation scripts
- End-user installation from complete binary bundle
- Added SGI Irix support (remote job execution with rsh only)
- Added Redhat 9.0 support - to deal with NPL problems
- Generic Linux installation for platforms other than Redhat 7.3
- Bug fixes in GUI
- Improved support for remote job execution
- Moved to hostname only resolution, no use of explicit IPs
- Improvements to HySS performance

Version 1.02a
=============

- Fixed bug with making connections between tasks in GUI
- Fixed file ownership problems for binary bundles in installation
- Fixed problem with absolute links in binary bundle (all linked files removed)
- Changed install script back to using csh rather than tcsh

Version 1.01a
=============

- Numerous bug fixes in GUI
- Added text to better document PHASER and TEXTAL tasks
- Fixed file permission problems for TEXTAL PERL scripts
- Improvements to HySS procedure

Version 1.0a
============

- First alpha test release