qFit 2024v3

qFit is a collection of programs for modeling multi-conformer protein structures.

Electron density maps obtained from high-resolution X-ray diffraction data are a spatial and temporal average of all conformations within the crystal. qFit evaluates an extremely large number of combinations of sidechain conformers, backbone fragments and small-molecule ligands to locally explain the electron density.

If you use this software, please cite:

• Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, & Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. eLife. (2024).
• Riley BT, Wankowicz SA, et al. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Sci. 30, 270–285 (2021)
• Keedy, D. A., Fraser, J. S. & van den Bedem, H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput. Biol. 11, e1004507 (2015)

qFit-ligand:

• Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo A, van den Bedem H,, Fraser J, Wankowicz SA.* (2024) Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments. BioRxiv.
• van Zundert, G. C. P. et al. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. 61, 11183–11198 (2018)

As this software relies on CVXPY, please also cite:

• Agrawal, Verschueren, Diamond, & Boyd. A Rewriting System for Convex Optimization Problems. Journal of Control and Decision. (2018).
• Diamond & Boyd. CVXPY: A Python-Embedded Modeling Language for Convex Optimization. Journal of Machine Learning Research. (2016)

Installation (conda recommended)

We recommend using the conda package manager to install qFit.

1. Clone the latest release of the qFit source, and install to your conda env

   git clone -b main https://github.com/ExcitedStates/qfit-3.0.git

   cd qfit-3.0

2. Create the Conda environment using the downloaded file:

   mamba env create -f environment.yml

3. After creating the Conda environment, activate it:

   conda activate qfit

4. If you installing on M1 Mac:

   conda activate qfit; conda env config vars set CONDA_SUBDIR=osx-64; conda deactivate conda activate qfit

Advanced

If you prefer to manage your environments using other methods, qFit has the following prerequisites:

• Python 3.6+
• numpy
• scipy
• cvxpy

Once dependencies are installed, you can clone the qFit source, and install to your env as above.

Usage examples

The qfit package comes with several command line tools to model alternate conformers into electron densities. You should select the command line tool that is most suited for your task. Please refer below for a basic usage example. More specialized and advanced use case examples are shown in example directory.

To remove single-conformer model bias, qFit should be used with a composite omit map. One way of generating such map is using the Phenix software suite:

phenix.composite_omit_map input.mtz model.pdb omit-type=refine

An example test case (1G8A) can be found in the qfit protein example directory. Additionally, you can find the cyroEM protein example(PDB: 7A4M) and the ligand example qFit-ligand example (PDB: 4MS6) in the example directory.

Recommended settings

To model alternate conformers for all residues in a X-ray crystallography model using qFit, the following command should be used:

qfit_protein [COMPOSITE_OMIT_MAP_FILE] -l [LABELS] [PDB_FILE] -p [# OF THREADS]

This command will produce a multiconformer model that spans the entirety of the input target protein. The final model, with consistent labeling of multiple conformers is output into multiconformer_model2.pdb. This file should then be used as input to the post-qFit refinement script provided in scripts folder.

qFit can be run on a single thread, but speeds up significantly with multiple threads. Do to this, use the -p flag.

If you wish to specify a different directory for the output, this can be done using the flag -d.

By default, qFit expects the labels FWT,PHWT to be present in the input map. Different labels can be set accordingly using the flag -l.

Using the example 18GA:

qfit_protein example/qfit_protein_example/composite_omit_map.mtz -l 2FOFCWT,PH2FOFCWT example/qfit_protein_example/1G8A_refine.pdb

After multiconformer_model2.pdb has been generated, refine this model using:

qfit_final_refine_xray.sh example/qfit_protein_example/18GA.mtz example/qfit_protein_example/multiconformer_model2.pdb

Additionally, the qFit_occupancy.params file must exist in the folder (this is an output of qFit protein).

Bear in mind that this final step currently depends on an existing installation of the Phenix software suite. This script is currently written to work with version Phenix 1.21.

To model alternate conformers for all residues in a cryo-EM model using qFit, the following command should be used:

qfit_protein [MAP_FILE] -r [RES] [PDB_FILE] -em qfit_protein example/qfit_cryoem_example/7A4M_box.ccp4 -r 1.7 example/qfit_cryoem_example/7A4M_box.pdb

After multiconformer_model2.pdb has been generated, refine this model using:

qfit_final_refine_cryoEM.sh example/qfit_cryoem_example/7A4M_box.ccp4 example/qfit_cryoem_example/multiconformer_model2.pdb example/qfit_cryoem_example/7A4M_box.pdb

More advanced features of qFit (modeling single residue, more advanced options, and further explainations) are explained in TUTORIAL.

To model alternate conformations of ligands using qFit, we recommend running composite omit map excluding bulk solvent with the following command:

phenix.composite_omit_map input.mtz model.pdb omit-type=refine exclude_bulk_solvent=True

qFit-ligand can be executed the following command:

qfit_ligand [COMPOSITE_OMIT_MAP_FILE] [PDB_FILE] -l [LABELS] [SELECTION] -sm [SMILES]

This command facilitates the incorporation of alternate ligand conformations into your protein model. The results are outputted to two files: multiconformer_ligand_bound_with_protein.pdb, which is the multiconformer model of the protein-ligand complex, and multiconformer_ligand_only.pdb, which is the multiconformer model of the ligand alone.

After running qFit-ligand, it is recommended to perform a final refinement using the script found in scripts. Run this in the same directory as your models.

If you wish to specify the number of ligand conformers for qFit to sample, use the flag -nc [NUM_CONFS]. The default number is set to 10,000.

Using the example 4MS6:

qfit_ligand example/qfit_ligand_example/4ms6_composit_map.mtz example/qfit_ligand_example/4ms6.pdb -l 2FOFCWT,PH2FOFCWT A,702 -sm 'C1C[C@H](NC1)C(=O)CCC(=O)N2CCC[C@H]2C(=O)O' -nc 10000

To refine multiconformer_ligand_bound_with_protein.pdb, use the following command

qfit_final_refine_ligand.sh 4ms6.mtz

Contributing

qFit uses Black to format its code and provides a git hook to verify that code is properly formatted before allowing you to commit.

Before creating a commit, you will have to perform two actions:

1. Install Black, either through a package manager or by running python3 -m pip install --user black
2. Run git config core.hooksPath .githooks/ to use the provided pre-commit hook

License

The code is licensed under the MIT licence (see LICENSE).

Several modules were taken from the pymmlib package, originally licensed under the Artistic License 2.0. See the licenses directory for a copy of the original source code and its full license.

The elements.py is licensed under MIT, Copyright (c) 2005-2015, Christoph Gohlke. See file header.

The Xpleo software and LoopTK package have been major inspirations for the inverse kinematics functionality.