diff --git a/README.md b/README.md index 3075d2e8..535bfad7 100644 --- a/README.md +++ b/README.md @@ -106,13 +106,13 @@ prank predict -c alphafold test.ds # use alphafold config and model (confi ### Prediction output - For each structure file `{struct_file}` in the dataset P2Rank produces several output files: + For each structure file `{struct_file}` in the dataset, P2Rank produces several output files: * `{struct_file}_predictions.csv`: contains an ordered list of predicted pockets, their scores, coordinates of their centers together with a list of adjacent residues, list of adjacent protein surface atoms, and a calibrated probability of being a ligand-binding site. * `{struct_file}_residues.csv`: contains a list of all residues from the input protein with their scores, mapping to predicted pockets, and a calibrated probability of being a ligand-binding residue. - * PyMol and ChimeraX visualizations in `visualizations/` directory (`.pml` and `.cxc` scripts with data files in `data/`) - * Generating visualizations can be turned off with the `-visualizations 0` parameter + * PyMol and ChimeraX visualizations in `visualizations/` directory (`.pml` and `.cxc` scripts with data files in `data/`). + * Generating visualizations can be turned off with the `-visualizations 0` parameter. * `-vis_renderers 'pymol,chimerax'` parameter can be used to turn individual visualization renderers on/off. * `-vis_copy_proteins 0` parameter can be used to turn off copying of protein structures to the visualizations directory (faster, but visualizations won't be portable). * Coordinates and ligandability scores of SAS points can be found in `visualizations/data/{struct_file}_points.pdb.gz`. Here, the "Residue sequence number" (23-26 of HETATM record) @@ -194,7 +194,7 @@ prank fpocket-rescore test.ds -fpocket_keep_output 0 # delete fpo In this case, the dataset file can be a simple list of pdb/cif files since Fpocket predictions will pe calculated ad-hoc. `prank fpocket-rescore` will produce `predictions.csv` as well, so it can be used as an in-place replacement for `prank predict` in most scenarios. -Note: if you use `fpocket-rescore`, please cite Fpocket paper as well. +Note: if you use `fpocket-rescore`, please cite Fpocket as well.