2024.3

What's Changed

The main change for this version is an improvement in ligand multiconformer modeling. Additionally, we have some code improvements in protein.

• Allow qFit to run with multiple backbone inputs by @stephaniewankowicz in #382
• add find_close_residues.py to setup.py by @stephaniewankowicz in #396
• fix argparse error in qfit_ligand.py by @jessicaflowers in #398
• 404 qfit residue is missing by @stephaniewankowicz in #407
• update for CVXPY citation by @stephaniewankowicz in #408
• Add p flag by @stephaniewankowicz in #409
• Add em to README.md example by @stephaniewankowicz in #411
• re-implementing conda & M1 instructions by @stephaniewankowicz in #412
• Add calc rscc to setup.py by @stephaniewankowicz in #413
• update default labels by @stephaniewankowicz in #417
• split QP into 3000 conformers by @stephaniewankowicz in #419
• update to be compatible with mac os for tests by @stephaniewankowicz in #422
• re-write em refinement by @stephaniewankowicz in #418
• Update README.md by @stephaniewankowicz in #421
• install using enviornment.yml by @stephaniewankowicz in #423
• Fix Complete Residue by @stephaniewankowicz in #424
• update order of readme by @stephaniewankowicz in #425
• Implement maxpool sampling by @stephaniewankowicz in #420
• Update em example by @stephaniewankowicz in #430
• Use deposited conformers if clashes by @stephaniewankowicz in #429
• set ci to use macos-13 by @dhogan-io in #431
• Edit test to fix macOS issues by @stephaniewankowicz in #427
• New qfit ligand by @jessicaflowers in #426
• Update ligand test by @jessicaflowers in #432
• Ligand additions by @jessicaflowers in #452
• formatting README by @stephaniewankowicz in #454
• Replacing 3K0N as the example, adding 1G8A by @stephaniewankowicz in #457
• Edit _zero_out_most_similar_conformer() to add the optional ability to add the occupancy of the conformer by @jessicaflowers in #459
• Update Refinement Phenix 2024 by @stephaniewankowicz in #458
• update ligand refine to remove low occ conformers by @stephaniewankowicz in #460
• Update lig_occ.py by @stephaniewankowicz in #461
• Maxpool fix by @stephaniewankowicz in #462
• remove duplicate rotamer sampling by @stephaniewankowicz in #463
• Restraint creation file in loop by @stephaniewankowicz in #466
• change qfit protein test by @stephaniewankowicz in #464
• add to ligand examples folder and scripts README by @jessicaflowers in #467
• correct comp omit for ligand by @stephaniewankowicz in #469
• Add bdc scaling for PanDDA models into ligand final refine script by @jessicaflowers in #471
• blackening all files by @stephaniewankowicz in #472
• fix calc_coord function by @stephaniewankowicz in #473
• Creating qFit version 2024.3 by @stephaniewankowicz in #475

Full Changelog: 2024.2...2024.3

2024.2

This release implements the move to open-sourced solvers for qFit. It is associated with the revision of Wankowicz et al 'Uncovering Protein Ensembles: Automated Multiconformer Building in X-ray Crystallography and CryoEM' eLife 2023.

2024v1

qFit version 2024 v1 is associated with the revision of Wankowicz et al 'Uncovering Protein Ensembles: Automated Multiconformer Building in X-ray Crystallography and CryoEM' eLife 2023.

qFit Algorithm Changes:

• updating chi sampling dof per iteration to 1 by @stephaniewankowicz in #365
• 347 explore smaller rotamer window by @stephaniewankowicz in #366
• 354 re work angle sampling to rotate 360 by @jessicaflowers in #367
• Re-implement open source solvers by @blake-riley in #363
• Updating BIC hyperparameter by @stephaniewankowicz in #369
• Correct crystal and scale info by @stephaniewankowicz in #370
• Combine qFit residue into qFit protein by @stephaniewankowicz in #371
• Removing the Phenix Aniso refinement option by @stephaniewankowicz in #372
• change isotropic sampling directions in backbone by @jessicaflowers in #379
• Split QP step into two in sample sidechain by @jessicaflowers in #389
• Adding Hetatms in output of multiconformer_model2 by @stephaniewankowicz in #393
• Solver Error Catches by @stephaniewankowicz in #383
• Collapsing conformers with the same coordinates by @stephaniewankowicz in #200
• change rmsd cutoff in qFit segment by @stephaniewankowicz in #281
• Add in B-factor sampling by @stephaniewankowicz in #289
• adding flag to only run qFit segment by @stephaniewankowicz in #298
• 301 reconfigure qfit segment by @stephaniewankowicz in #306
• Updating hardcoded alt locs in backbone collapse by @stephaniewankowicz in #311
• qscore cutoff option for EM structures by @stephaniewankowicz in #317
• updating OXT issues by @stephaniewankowicz in #318
• updating write intermediate conformers argument by @stephaniewankowicz in #321
• Unify map extraction: use --padding option (and default value) in QFitSegment by @blake-riley in #327
• 177-qFit to work for EM with appropriate SF by @stephaniewankowicz in #322
• Segment BIC criteria = nconfs by @stephaniewankowicz in #341

Post qFit refinement/analysis scripts:

• move where we add hydrogens to after while loop by @stephaniewankowicz in #296
• adding reduce failure flag by @stephaniewankowicz in #297
• adding order solvent picking in refinement by @stephaniewankowicz in #303
• 301 re create refinement script to group occupancy of segment alt locs by @stephaniewankowicz in #304
• adding target weight params to final refine by @stephaniewankowicz in #310
• create all rotamers script by @stephaniewankowicz in #307
• Updating Ligand Occupany script to extract average b-factor by @stephaniewankowicz in #387
• Add rscc script by @stephaniewankowicz in https://github.com/ExcitedStdStates/qfit-3.0/pull/388

Other Maintenence for qFit Repository:

• Improve the example folder and README file by @ashrayar in #278
• Rename TUTORIAL.md to README.md by @stephaniewankowicz in #294
• Implementing faster qFit Ligand test by @stephaniewankowicz in #291
• updating numpy and python versions to work on M1 Macs by @stephaniewankowicz in #358
• Moving M1 change to Main by @stephaniewankowicz in #359
• Improved Error Message when CPLEX is not installed by @stephaniewankowicz in #362

Full Changelog: latest...2024v1

qFit version 3.2.2

What's Changed

• Fix CI after master-to-main switch by @blake-riley in #162
• Update README.md by @ashrayar in #161
• Update README in main by @blake-riley in #163
• Analysis script updates by @stephaniewankowicz in #168
• a post refine script that works! by @stephaniewankowicz in #169
• Improve README for M1 Macs by @blake-riley in #174
• Make sure the user provides a resolution value if the input map is in MRC/CCP4 or MAP formats by @ashrayar in #180
• Unify all QFitOptions classes into a single class by @ss199514 in #178
• Fixing large maps being able to be fed into qFit Protein without crashing by @stephaniewankowicz in #176
• If options.nproc is 1, run QFitRotamericResidue job in MainProcess by @blake-riley in #185
• 179 qfit protein outputting duplicate hetatms by @blake-riley in #186
• Clarify warning about AttributeError at Cβ by @blake-riley in #187
• Fixed X-ray data labels search and changed how phenix refinement parameters are given in post qfit refinement xray script by @ashrayar in #188
• Fix multiconformer_model.pdb not found error when it is actually present by @blake-riley in #196
• 189 delete qfit combine qfit ppidesign qfit segment and other entrypoints that dont work by @ashrayar in #197
• Fix post analysis script typos by @stephaniewankowicz in #193
• Better error message map/model are in the incorrect order upon input. by @stephaniewankowicz in #192
• Small patch fixes by @stephaniewankowicz in #195
• removing lines by @stephaniewankowicz in #201
• If a residue-sampling checkpoint exists, don't add it to the list of residues to be sampled by @blake-riley in #211
• Instruct users to install qFit from main branch code by @blake-riley in #212
• Rewrite XMap.extract() for 500x speed boost by @blake-riley in #214
• Fix non-convex objective errors by selectively deleting conformers by @blake-riley in #213
• Delete SpaceGroups.py by @stephaniewankowicz in #218
• Improved error message: unknown file type error in qfit residue by @stephaniewankowicz in #220
• Refine script: output names and riding hydrogens by @stephaniewankowicz in #221
• 226 create test to read in and write out map file by @stephaniewankowicz in #228
• 227 Building tests for a variety of SG by @ss199514 in #229
• 224 create a test to read in different model files by @ashrayar in #232
• Change branch: 226 create test to read inwrite out map file by @stephaniewankowicz in #239
• qFit 3.2.2: Merging dev -> main by @stephaniewankowicz in #237
• Update README.md by @stephaniewankowicz in #240

New Contributors

• @ashrayar made their first contribution in #161
• @ss199514 made their first contribution in #178

Full Changelog: v3.2.1...v3.2.2

v3.2.1

Release v3.2.1

What's Changed

• Update README.md for new refinement script/input by @stephaniewankowicz in #120
• Improve flags (& --help) of qfit programs by @blake-riley in #122
• Add --random-seed to provide option for reproducible runs by @blake-riley in #124
• Add --rmsd-cutoff option to qFit-ligand by @stephaniewankowicz in #126
• Update setup-miniconda GitHub Action (repairs failing CI) by @stephaniewankowicz in #129
• Fixing CI Testing function by @stephaniewankowicz in #137
• Changing write-intermediate-conformers argument to match qfit_protein by @stephaniewankowicz in #127
• Add Ca option in b-factor.py script by @stephaniewankowicz in #131
• Added cryo-EM and qFit ligand examples by @stephaniewankowicz in #125
• Fix CI, installs failing caused by numpy API change by @blake-riley in #148
• adding new post qfit analysis scripts by @stephaniewankowicz in #146
• correcting line for post qFit refine cryoEM by @stephaniewankowicz in #152
• Fixup indentation in alpha_rmsd by @blake-riley in #155
• adding qfit_protein for scale/cryst by @stephaniewankowicz in #151
• Move to python 3.7, 3.8 by @blake-riley in #156
• Remove licences, update citation by @blake-riley in #157
• Release bugfix version: 3.2.1 by @blake-riley in #158

Full Changelog: v3.2.0...v3.2.1

qFit version 2023 v1

What's Changed

qFit version 2023 v1 is associated with Wankowicz et al 'Uncovering Protein Ensembles: Automated Multiconformer Building in X-ray Crystallography and CryoEM'. The changes in that paper are outlined in this version release and qFit 3.2.2

Main updates to qFit algorithm

• Add --random-seed to provide an option for reproducible runs by @blake-riley in #124

Update to post qFit analysis scripts

• Update README.md for new refinement script/input by @stephaniewankowicz in #120
• Add Ca option in b-factor.py script by @stephaniewankowicz in #131

Coding update to qFit algorithm

• Improve flags (& --help) of qfit programs by @blake-riley in #122
• Add --rmsd-cutoff option to qFit-ligand by @stephaniewankowicz in #126
• adding new post qfit analysis scripts by @stephaniewankowicz in #146
• adding qfit_protein for scale/cryst by @stephaniewankowicz in #151

Other Maintenence for qFit Repository

• Remove licences, update citation by @blake-riley in #157
• Move to python 3.7, 3.8 by @blake-riley in #156
• Update setup-miniconda GitHub Action (repairs failing CI) by @stephaniewankowicz in #129
• Fix CI, installs failing caused by numpy API change by @blake-riley in #148
• Fixing CI Testing function by @stephaniewankowicz in #137
• Changing write-intermediate-conformers argument to match qfit_protein by @stephaniewankowicz in #127
• Added cryo-EM and qFit ligand examples by @stephaniewankowicz in #125
• correcting line for post qFit refine cryoEM by @stephaniewankowicz in #152
• Fixup indentation in alpha_rmsd by @blake-riley in #155
• Release bugfix version: 3.2.1 by @blake-riley in #158

Full Changelog: v3.2.0...latest

v3.2.0

Release v3.2.0
In line with https://www.biorxiv.org/content/10.1101/2020.09.03.280222v1