Doppio Release Notes

Version 1.3.0

14th May 2025

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

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

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

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

27th March 2025

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

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

29th January 2025

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

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

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

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

1st October 2024

Add em_placement jobs compatible with CCP4 9.0
Add Pipeliner Run External Program job to allow more flexible calling of external programs

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

4th June 2024

Add token-based user authentication system to secure server against unauthorised access

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.