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