=================
CCP-EM CHANGE LOG
=================

==============================
Changes for 1.6.0 (2022-04-07)
==============================

*) Use new Servalcat wrapper for Refmac
    This adds improved map sharpening, symmetry handling and difference maps,
    among other features. Details in Yamashita et al. (2021) Acta Cryst D77
    https://doi.org/10.1107/S2059798321009475

*) Improve Model Validation task with new methods 
    (https://doi.org/10.1107/S205979832101278X),
    bug fixes and updates to plots

*) Add FDR Model Validation task (https://doi.org/10.3389/fmolb.2021.652530)

*) Add Privateer (https://doi.org/10.3762/bjoc.16.204)

*) Add 3D Strudel (https://doi.org/10.1101/2021.12.16.472999)

*) Add PI-score (https://doi.org/10.1038/s41467-021-23692-x)

*) Buccaneer and Nautilus tasks updated to use Servalcat for refinement

*) Coot updated to v0.9.8.1

*) Fix Gatekeeper issues on OS X Catalina

*) Fix libfontconfig errors on recent Linux versions

*) Remove ConKit

*) Bug fixes:
    - Fix Haruspex map scaling bug
    - Fix setup script to find CCP4 v7.1 on Mac
    - Fix blank RELION GUI on Mac OS 11 Big Sur
    - Fix ChimeraX launching on Linux
    - Many other minor bug fixes and improvements

==============================
Changes for 1.5.0 (2020-10-29)
==============================

*) Add cryoEF task for determination of completeness of particle orientations

*) Add SIDESPLITTER executable and wrapper for use from RELION 3.1

*) Add EMDA programs and Python package for difference and average map
    calculations

*) Add Haruspex task in alpha mode (needs tensorflow installed via
    `ccpem-python -m pip`)

*) Add task for generating maps from atomic models

*) Add AceDRG task for generating ligand dictionary files

*) RELION - updated to version 3.1

*) Coot - updated to version 0.9.2-pre

*) LocScale: Use Gemmi for MTZ to MRC conversion
    Fixes issue with map grid  dimensions with prime factors larger than 19

*) Add B-factor analysis in Validation:Model task

*) Improvements to TEMPy difference map and SMOC tasks

*) Bug fixes:
    - Fixed MapProcess downsample option
    - Fixed bug where the last edit was ignored when running a new job
    - Fixed database error when running more than 256 jobs in a project
    - Various other minor bugs fixed

==============================
Changes for 1.4.1 (2019-11-25)
==============================

*) Fix bug in CCP-EM install script when CCP4 version >= 7.0.078 is installed

==============================
Changes for 1.4.0 (2019-11-14)
==============================

*) LAFTER - new task for local map denoising
    Details in Ramlaul, Palmer & Aylett (2019) J Struct Biol 205:30-40
    https://doi.org/10.1016/j.jsb.2018.11.011

*) Confidence Maps - new task for calculating confidence maps using False
    Discovery Rate control or other error criteria
    Details in Beckers, Jakobi & Sachse (2019) IUCrJ 6:18-33
    https://doi.org/10.1107/S2052252518014434

*) Model Validation - new task for running many model validation tools
    Includes Molprobity and CaBLAM for evaluating model geometry
    Refmac5 (model-map FSC, FSCavg) and TEMPy SMOC score for model fit in map
    Jpred to evaluate agreement with sequence based secondary structure prediction
    Link to Coot for fixing outliers

*) GUI updates:
    Add buttons to run Coot, RELION and relion_display from the main window
    Add PyMOL button in task toolbar
    RIBFIND output files now sorted and labelled more clearly in the Launcher
    Fix RIBFIND cluster table when number of rigid body segments is very large
    Various other minor improvements

*) MRC to MTZ improvements:
    All sharpened and blurred maps now loaded into Coot correctly
    Fixed resolution scale on output plots
    Plot generation made more robust

*) Coot - updated to latest 0.9-pre version, including fix for Curlew

*) TEMPy Diffmap - Local scaling option added

*) ccpem-python - gemmi and pip modules added

*) RELION - updated to version 3.0.8

*) Update versions of many bundled libraries

*) Various minor bug fixes

==============================
Changes for 1.3.0 (2019-04-08)
==============================

*) RELION - updated to version 3.0.4.

    As with the previous v2.1, OpenMPI is included for running parallel jobs
    on a single computer, and on Linux, RELION is compiled with CUDA support
    so GPU acceleration should work correctly.

*) Coot - updated to version 0.9-pre ("refinement" branch)
    Many improved features for working with cryo-EM maps.

    Note that on Mac OS X, Coot requires the latest version of XQuartz
    (2.7.11).

*) ProSHADE - new task for map symmetry determination, map reboxing and
    other functions.

*) SymmetryExpand - new task. Uses Refmac to copy changes from one chain to
    symmetry-related copies

*) Buccaneer & Nautilus - added results summary graphs
    Minor pipeline improvements

*) Refmac - fix FSC calculation bug in half-map validation pipeline
    Various GUI improvements

*) MRC to MTZ - plot output improved. Handling of sharpening/blurring factors
    made consistent with Refmac, Buccaneer and Nautilus tasks.

*) RIBFIND (FlexEM) updated to deal with multi-chain PDBs

*) OpenMPI - rename the previous 'mpirun' wrapper script to 'ccpem-mpirun'.
    This avoids any conflict with other MPI installations.

*) Update versions of many bundled libraries

*) Bug fixes:
    PATH order - On Mac OS X, CCP-EM programs are now found in preference to
      CCP4 ones with the same name. This makes behaviour on Mac OS X the same
      as on Linux.
    Fix bug where CCP-EM would fail to start if the project database could not
      be opened.
    Fix for local refinement mode in Refmac on Mac (external, requires update
      to CCP4 version 7.0.072)
    Fix illegal instruction error in FFTW3 library
    Fix scrolling and text positioning bugs in log output panel

*) Add LAFTER, FDR control and model validation tasks in alpha mode

*) Various other minor improvements

*) Known bugs:
    On Mac, Coot's download functions (e.g. fetch from PDB) don't work
    Refmac pipeline fails to preserve LINK records for metal ions

==============================
Changes for 1.2.0 (2018-12-18)
==============================

*) RELION - a pre-compiled copy of RELION v2.1 is now included in the suite

    This includes OpenMPI for running on a single computer. To run efficiently
    on clusters, you should still use a copy of RELION that is compiled
    specifically for each system. In that case, be careful when you set up
    your PATH to ensure the desired version of RELION is found first.

    On Linux, RELION is compiled with CUDA support, so GPU acceleration should
    work correctly.

*) LocScale - now works in MPI mode on both Mac OS X and Linux

*) Refmac - add option for automatic detection of symmetry in atomic models,
    and use of symmetry restraints.

*) Buccaneer - use EM reference structure

*) MRC to MTZ - fix bug with empty lists in sharpen and blur fields

*) TEMPy scores - task included to rank fitted models based on multiple scores.

*) TEMPy Local score - now evaluates atomic model fit on either small residue 
    fragments or relatively large rigid-bodies, based on map resolution.

*) Installation script - check CCP4 version is up to date

*) Various other bug fixes

==============================
Changes for 1.1.0 (2018-07-24)
==============================

*) LocScale now available in CCPEM GUI without external dependencies
    Calculate reference map from input structure using Refmac
    Use MapMask to enforce x,y,z axis order as input to LocScale
    Use np_locscale branch
    Take out of alpha mode
    Add mpi4py support

*) Update DockEM
    Improve GUI
    Multiprocessing option
    Show search region in Chimera

*) Flex-EM option to auto generate rigid body input
    Calls ribfind task to generate rigid body if not supplied
    JSmol window removed

*) Ribfind GUI simplified
    JSmol window removed
    Fixed cutoffs used for generation of rigid body outputs

*) Update toolbar
    Remove 'Load' button
    Rename 'New' to 'Clone'
    Update icon set, make Run button more obvious
    Resize icons for correct display on Mac retina screens

*) Fix main GUI crash bug when in alpha mode and modeller not available

*) Tag CCP-EM version details to all CCP-EM process logs

==========================
Version 1.0.0 (2018-04-09)
==========================

This change log starts from the first stable release of CCP-EM, version 1.0.0.
An overview of the main functionality of the suite can be found here:
https://doi.org/10.1107/S2059798317007859
