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