Doppio Release Notes ==================== Version 1.3.0 ------------- *14th May 2025* New jobs ^^^^^^^^ * Add all jobs for the full RELION 5 sub-tomogram averaging pipeline * Add EulerMate job to import sub-tomogram particle coordinates and orientations from IMOD model files * Add ProSMART job for generating atomic distance restraints for protein and nucleic acid chains * Add MetalCoord job for generating restraints for coordinated metal ions Job updates ^^^^^^^^^^^ * Add visualisation scripts for loading output of LocScale, Model Validation and Fetch from AlphaFold DB jobs in Coot and ChimeraX * Update options for AceDRG job to allow ligands with metal ions, more input types and more control of AceDRG behaviour * Check for masked maps that would cause confidence map calculation to fail in Model Validation job * Improve validation of rescaling options in Bayesian Particle Polishing job * Fix bug running Join STAR Files job * Update em_placement jobs to warn if incompatible program versions are found * Update various job results to use Doppio's new interactive image viewer Doppio updates ^^^^^^^^^^^^^^ * Change to use Conda Constructor to make Doppio installer packages * Add ability to install additional software packages from Doppio GUI * Add interactive image viewer to allow browsing of images and volumes in job results * Add ability to run custom scripts when launching Coot, Chimera or ChimeraX * Update to use Python 3.9, Node 20 and Electron 35 * Package fonts with Doppio so it can be used completely offline Pipeliner updates ^^^^^^^^^^^^^^^^^ * Update EMDB and EMPIAR deposition features following feedback and collaboration with EMBL-EBI * Improve validation of job running options * Update Python version compatibility to 3.9 - 3.13 * Various other minor bug fixes and updates Version 1.2.1 ------------- *27th March 2025* New jobs ^^^^^^^^ * Add Servalcat Refine job for atomic model refinement with Servalcat. This will eventually replace the Refmac Servalcat job. * Add Servalcat Mask from Model job to create masks from atomic models Job updates ^^^^^^^^^^^ * Fix error setting the Python interpreter to use when running the RELION 4 class ranker * Remove erroneous logfile.pdf output node from Topaz Train job * Fix bug using multiple MPI procs and improve option validation in Bayesian Polish job * Improve results displays for Pipeliner Class Select job * Fix minor bugs in Model Validation results display Doppio updates ^^^^^^^^^^^^^^ * Update Moorhen to v0.18.1 * Update versions of some dependencies Pipeliner updates ^^^^^^^^^^^^^^^^^ * Use standard Python logging rather than printing to stdout and stderr * Update versions of some dependencies * Switch to use pyproject.toml file for Python packaging metadata * Minor improvements to scripting API * Improve validation of job options used for executable commands Version 1.2.0 ------------- *29th January 2025* New jobs ^^^^^^^^ * Add CryoDRGN jobs for heterogeneous reconstruction, homogeneous reconstruction and interactive subset selection * Add CryoVAE and CryoDANN jobs for particle denoising and filtering * Add RELION Symmetry Expansion job Job updates ^^^^^^^^^^^ * Fix use of an external config file, CPU and GPU options in crYOLO job * Add option for reference structure input in em_placement job * Show output rather than input maps in em_placement job results * Fix results from EMDA mask creation job and make compatible with EMDA2 * Fix bug validating existence of imported micrographs in Import job * Add Feature Enhance mode and advanced options in LocScale job * Expand results table in ModelAngelo job * Add table of percentiles for model-to-map fit scores in Model Validation job * Add particle image results display in Particle Subtraction job * Fix bug where CTF correction was ignored in Reconstruct job * Relabel, rearrange and expand help text for many options in Refmac Servalcat job * Add options for keyword input, external restraints and hydrogen atom handling in Refmac Servalcat job * Fix bug showing results from Refmac Servalcat job when input and output filenames are the same * Add refinement statistics table and B-factor distribution plot in Refmac Servalcat job results * Fix bug with PDB input files to RIBFIND job * Update Process Predicted Model and Slice jobs for latest CCP4 9.0 Doppio updates ^^^^^^^^^^^^^^ * Improve interactive class selection tool to find correct optimiser file and allow job alias to be set * Update Moorhen to v0.14.1 * Add ability to open MTZ files in Moorhen * Add menu in Moorhen to open files from the Doppio project * Add base URL setting for running Doppio behind a proxy server or alongside other services * Warn users that job deletion might also delete other dependent jobs * Fix validation messages for conditionally-required job options * Keep RELION 5 job options visible (but deactivated) when RELION 4 is found Pipeliner updates ^^^^^^^^^^^^^^^^^ * Substitute environment variables in all job commands * Check for immediate errors when running queue submission commands * Add missing nodes when creating archives and metadata reports from projects imported from RELION * Print warnings if queue submission script looks like a RELION-style one * Avoid spurious warnings about qsub extra options in Pipeliner settings file * Various other minor bug fixes and improvements Version 1.1.0 ------------- *1st October 2024* New jobs ^^^^^^^^ * Add em_placement jobs compatible with CCP4 9.0 * Add Pipeliner Run External Program job to allow more flexible calling of external programs Job updates ^^^^^^^^^^^ * Update ModelAngelo job for full compatibility with RELION * Use RELION 5's copies of Topaz, ModelAngelo and class ranker by default, if installed * Rename Import jobs for greater clarity * Make Fetch job more robust * Add validation checks in CtfFind job to help select appropriate options according to what output was written by the MotionCorr job * Remove support for running Gctf in new CtfFind jobs * Add option to validate the existence of output files in Import, MotionCorr and CtfFind jobs * Improve options for Topaz helical particle picking * Combine Extract and Reextract jobs into a single Extract job * Combine CtfRefine refinements into a single job * Add option to reconstruct half maps in the Reconstruct job * Improve options for Lafter job * Fix bug in JoinStar job if input files had the same name * Fix bug with mismatched file names in Random Select job Doppio updates ^^^^^^^^^^^^^^ * Add tool for interactive 2D and 3D class selection within Doppio * Update job status more quickly when jobs start and finish running * Show the reason why jobs are unavailable * Make API check timeout into a user-configurable setting * Prevent page header splitting into multiple lines when window width is reduced * Add exit confirmation dialog when closing full-screen viewers such as Moorhen * Update Moorhen to v0.9.0 * Show summaries of node contents for the main node types in the job I/O tab Pipeliner updates ^^^^^^^^^^^^^^^^^ * Fix bug where project info was occasionally lost and overwritten * Fix bugs in handling quoted or illegal values in STAR files * Various other minor bug fixes Version 1.0.1 ------------- *4th June 2024* * Add token-based user authentication system to secure server against unauthorised access Version 1.0.0 ------------- *26th April 2024* Initial stable release! 🎉 This and all previous versions had a serious security flaw, please update to later versions as soon as possible.