Merge pull request #409 from ExcitedStates/add_p_flag

Add p flag

README.md

@@ -40,7 +40,6 @@ Once these are installed, you can:
 
 1. You're now ready to run qFit programs! See [usage examples](#sec:usage-examples) below for some examples.
 
-
 ### Advanced
 
 If you prefer to manage your environments using other methods, qFit has the following prerequisites:
@@ -81,12 +80,14 @@ An example test case (3K0N) can be found in the [qfit protein example](example/q
 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]`
+`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](scripts/post) folder.
+be used as input to the post-qFit refinement script provided in [scripts](scripts/post) folder. 
+
+qFit can be run on a single thread, but speeds up significantly with multiple threads.
 
 If you wish to specify a different directory for the output, this can be done
 using the flag *-d*.

scripts/post/README.md

@@ -3,6 +3,7 @@
 ![](https://github.com/ExcitedStates/qfit-3.0/workflows/tests/badge.svg)
 
 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. (2023).](https://www.biorxiv.org/content/10.1101/2023.06.28.546963v2.abstract)
 - [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)](https://dx.doi.org/10.1002/pro.4001)
 - [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)](https://dx.doi.org/10.1021/acs.jmedchem.8b01292)
 - [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)](https://dx.doi.org/10.1371/journal.pcbi.1004507)

setup.py

@@ -37,8 +37,8 @@ def main():
     setup(
         name="qfit",
         use_scm_version=True,
-        author="Blake Riley, Stephanie A. Wankowicz, Gydo C.P. van Zundert, Saulo H.P. de Oliveira, and Henry van den Bedem",
-        author_email="saulo@stanford.edu",
+        author="Stephanie A. Wankowicz, Blake Riley, Gydo C.P. van Zundert, Saulo H.P. de Oliveira, and Henry van den Bedem",
+        author_email="mullane.stephanie@gmail.com",
         project_urls={"Documentation": "https://github.com/ExcitedStates/qfit-3.0/"},
         package_dir=package_dir,
         packages=packages,