Below is the list of features added in each version.
0.0.x
0.1.x
0.2.x
0.2.1 (Babimost)
Interquartile-based e.s.u. and the side chain torsion comparison tool. Several bugfixes.
0.2.2 (Baborow)
NCS refinement in refmac and pre-start verification of the CCP4 configuration.
0.2.3 (Baranow Sandomierski)
Phenix refinement (so far with default parameters).
0.2.4 (Barcin)
Polar contact analysis across structures.
0.2.5 (Barczewo)
Database lock. Average structure output with ANISOU records representing covariance.
0.2.6 (Bardo)
Results window now shows various lists, including phi/psi and chi angles, atoms with refined occupancy, atom polar contacts and geometric parameters. The job results dialog has been retired.
0.2.7 (Barlinek)
The new dialog is implemented in the results window which shows all the ensemble outliers. Also, the results window now lists the percentile-based spread.
0.2.8 (Bartoszyce)
The percentile-based spread analysis window is implemented. It goes beyond what shakerr does and allows general structural comparisons of models, but it will operate on ensembles too. Documentation describing it will be coming.
0.2.9 (Barwice)
ProteinRanger is now available to run outside ShakErr as separate application.
0.2.10 (Belchatow)
Cluster analysis to repair problematic residues in model ensembles.
0.2.11 (Belzyce)
Import outside tarballs as jobs. Run jobs using model ensemble as a starting point (i.e. instead of autogenerated noised models). Open model ensemble and (optionally) maps in Coot. Scoop up the coot output as new job. Several bugfixes and strict dependency enforcement upon installation.
0.2.12 (Bedzin)
Ensemble completion feature - residues with missing atoms can be fixed automatically.
0.2.13 (Biala)
R.M.S.D. cutoff for ensemble repair, info tab.
0.2.14 (Biala Piska)
PBS refinement. An overhaul of the model and ensemble classes, everything now should be faster and less memory-greedy.
0.2.15 (Biala Podlaska)
Several bugfixes. Cross-ensemble PBS calculation.
0.2.16 (Biala Rawska)
PBS calculation for structural homologues (relies on SSM implementation in superpose).
0.2.17 (Bialobrzegi)
Several bugfixes. Regularization with refmac, spread-vs-quantile plot.
0.2.18 (Bialogard)
Some bugfixes. Outlier shift estimate and water match option in Protein Ranger.
0.2.19 (Bialy Bor)
Grouped p.b.s./r.m.s.d. now includes protein backbone, sidechains, heteroatoms and waters. Now also applies to ProteinRanger.
0.2.20 (Bialystok)
Some bugfixes. Z-score B-factor column output in ProteinRanger. Also, the command-line version of ProteinRanger, PBScalculator, is included and will be installed automatically and accessible from command line as pbscalc. Description can be found here.
0.2.21 (Biecz)
Z-score plot implemented in ProteinRanger.
0.2.22 (Bielawa)
The atom shift-vs-distance from a residue plot in ProteinRanger.
0.2.23 (Bielsk Podlaski)
r.m.s.d. plots moved to Matplotlib.
0.2.24 (Bielsko Biala)
Model variance plotting features.
0.2.25 (Bierun)
Model error calculation for Fc (clipper-based).
0.2.26 (Bierutow)
Residue type selection and sorted plot option for e.s.u. plotting.
0.2.27 (Biezun)
Clipboard export implemented for model variance plots.
0.2.28 (Bilgoraj)
Several minor fixes and randomization of intensities. requires ctruncate or use of the newly implemented internal conversion algorithm.
0.2.29 (Biskupiec)
Multi-run setup and job stopper.
0.2.30 (Bisztynek)
Fixes the PDB download bug caused by corrupt cif-files (_diffrn.details).
0.2.31 (Blachownia)
Choice of solvent correction in refmac refinement.
0.2.32 (Blaszki)
Variable test set and seeding in multi-job dialog.
0.2.33 (Blazowa)
Matching the alternate conformers by their spatial positions (for now, only proteins and for not more than two conformers.
0.2.34 (Blonie)
Several bugfixes. Improved refinement software parameters setup (plus several more phenix parameters). Output of split conformers in the Z-score chart.
0.2.35 (Bobolice)
Bugfixes and editing the project/job titles.
0.2.36 (Bobowa)
Bugfixes and toggling of strict residue name matching in pbs calculation. Thus includes the new version of the command line pbs calculator.
0.2.37 (Bochnia)
Bugfixes and export/import of job lists in multirun dialog.
0.2.38 (Bodzentyn)
Ability to hide individual projects from the list.
0.2.39 (Bogatynia)
The command line access implemented via pyshakerr.command module.
0.2.40 (Boguchwala)
Various bugfixes. Modeling of the error inflation.
0.2.41 (Boguszow-Gorce)
Several bugfixes and changes to command, pdbtool and pymtz modules.
0.2.42 (Bojanowo)
Many bugfixes and additions, mostly under the hood. ASP/GLU protonation analysis added to the GUI.
0.2.43 (Boleslawiec)
Several updates to command module: run analyze plugins, output esd lists, multi-model pdb output, phi-psi/chi/polar distance comparison, chain extraction
rmsdFrame as standalone application (some bugs remain)
Bonferroni corrections for target scores (everything targeted at P=0.05)
Better sorting in Z-dialogs and better filtering of polar contacts
Model import from pdb_redo
Ca-Ca comparison graph
0.2.44 (Bolkow)
Some bugfixes. Main addition is the command line interface:
shakerun
shakalyze
shakompare