Author(s)

• pathwalker: Matthew Baker

Purpose

Build a model with path walking

How pathwalker works:

Examples

Standard run of pathwalker:

Running pathwalker is easy. From the command-line you can type:

phenix.pathwalker my_map.mrc resolution=3 threshold=0.2 nres=150

This will build a model based on the map my_map.mrc at a resolution of 3 A using a threshold of 0.2 and looking for 150 CA atoms

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• input_files
  • map_file = None File with CCP4-style map. May have origin in any location.
• default_params
  • threshold = None Threshold used for populating pseudatoms.
  • nres = None Number of pseudoams to populate the density with
• strategy
  • seq_file = None Sequence file
  • pa_file = None Optional input pseudoatoms to be used as starting point for pathwalker to be run. This model should be in the same reference frame as the input map unless starting_model_is_from_box_map_au is set.
  • start_pt = 0 If a pa_file is used, does the user want to specify a start PA. Must be used in conjunction with end_pt.
  • end_pt = 0 If a pa_file is used, does the user want to specify a end PA. Must be used in conjunction with start_pt.
  • verbose = False Verbose turns on path evaluation.
  • tsp = *ortools LKH TSP solver to be used.
  • pa_type = *kmeans sc ac ms gmm birch PA type used for populating pseudatoms. (kmeans is default)
  • noise = 0 Add noise to atom positions (float)
  • map_weight = False Weighting distances by map value
  • filter = False Apply a filter to the map. Defualt is 4.5A, if turned on. This may help with PA placement
  • filter_resolution = 4.5 Resolution to apply a filter. The default is 4.5A if turned on.
  • or_time = 30 Time (in second) to allow OR tools to refine pathwalker trace Default is 30 seconds
  • local_search_strategy = *GUIDED_LOCAL_SEARCH AUTOMATIC GREEDY_DESCENT SIMULATED_ANNEALING TABU_SEARCH OBJECTIVE_TABU_SEARCH Local search strategies (also called metaheuristics) for the OR-Tools TSP solver.
  • prob_model = False compute a probabilistic model based on multiple pathwalker paths.
  • all_atom = False Convert the final pathwalker model into an all-atom model using Pulchra.
  • reverse = False Geneate the all-atom reverse path with Pulchara
  • refine_resolution = 0 Add a map resolution value to run real-space refinement
  • refine_cycles = 5 The number of real space refinement cycles that are to be run.
  • bracket = [] This handles the options for iterative PA generation and tsp solver. Three values are required: Threshold minimum Threshold maximum Threshold step They should be entered like bracket=0.22,0.24,0.01
  • tsp_runs = [0] Number of TSP runs and the amount of noise to apply to each run. for example: tsp_runs=0,0,0,1,0 will actually create 5 models, where runs 1-3 and 5 have no addative noise, while run 4 has noise equivalent to 1 sigma added to the original PAs
  • average_model = False if multiple TSP runs are set, an average model can be genreated with this flag
• output_files
  • pw_out_pdb = pw-threshold.pdb Search PDB file, transformed to superpose on the target map file.
  • pts_out_pdb = pts-threshold.pdb Search PDB file, transformed to superpose on the target map file.
  • pts_out = pts.txt Pseudoatom points generated (coordinates)
• guiGUI-specific parameter required for output directory
  • output_dir = None