Releases: ExcitedStates/qfit-3.0
2024.2
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
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