Cryo-EM Map Best Structure Search from WEMD Simulation
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Role-based/Structural Biologist
Solution-based/Target Identification/Target Preparation
Task-based/Target Prep & Analysis/Protein Preparation
Product-based/Molecular Dynamics/WESTPA
Description
This floe generates cryogenic electron microscopy (cryo-EM) density maps for each conformer selected from WEMD simulation trajectories. It also finds the best candidates to match the reference map experiments by calculating correlation coefficients between simulated and experimental maps. Multiple reference maps can be input and matched at the same time.
Promoted Parameters
Title in user interface (promoted name)
Input Data for Simulation
Collection (collection): Protein sampling data generated from previous weighted ensemble MD simulations. Only one WEMD collection is created for a series of WEMD simulations for the same system and setting.
Required
Type: collection_source
Default: wemd_simulation_collection
Input Cryo-EM Maps and Options for Best Structures Search
Cryo-EM Map Resolution (resolution): Resolution of the input cryo-EM maps (angstroms).
Required
Type: decimal
Default: 2.0
Reference Protein Dataset after SPRUCE Preparation (ref_dataset): Input Dataset for Reference Protein (structure must be fit to the input cryo-EM maps).
Required
Type: data_source
Superposition method (superpose_method): Superposition method to fit simulation structure to reference structure of cryo-EM map.
Required
Type: string
Default: GlobalSequence
Choices: [‘GlobalSequence’, ‘SiteSequence’, ‘DDMatrix’, ‘SSE’, ‘SiteHopper’]
Selected Components for Cryo-EM Map (mask_components): Selected components to generate simulated maps from simulation trajectories.
Required
Type: string
Default: [‘protein’, ‘nucleic’, ‘ligand’]
Choices: [‘protein’, ‘nucleic’, ‘ligand’, ‘solvent’, ‘metals’, ‘counter_ions’, ‘lipids’, ‘packing_residues’, ‘sugars’, ‘undefined’, ‘cofactors’, ‘excipients’, ‘polymers’, ‘post_translational’, ‘other_proteins’, ‘other_nucleics’, ‘other_ligands’, ‘other_cofactors’]
Cryo-EM Map Files (map_files): Input cryo-EM map files for best structure search (in .mrc format).
Required
Type: file_in
Resize Cryo-EM Map(s) (resize_map): Toggle on to resize cryo-EM map(s) using reference structure(s) with 10 angstroms of padding.
Type: boolean
Default: True
Choices: [True, False]
Masking options for RSCC
Masking Control (masking_control): Toggle on to mask simulated and reference cryo-EM maps.
Type: boolean
Default: True
Choices: [True, False]
Masking Scheme for Reference Cryo-EM Map (masking_scheme_ref): Options for masking reference cryo-EM map: “all”, include everything; “threshold”, density value below the specified value will be masked out; “std”, density value below the specified standard deviations above the mean will be masked out.
Type: string
Default: threshold
Choices: [‘all’, ‘threshold’, ‘std’]
Masking Value for Reference Cryo-EM Map (masking_level_ref): Input value for mask definition: for “threshold”, value below which to mask out; for “std”, standard deviations above the mean below which to mask out.
Type: decimal
Default: 0.0
Masking Scheme for Simulated Cryo-EM Map (masking_scheme_traj): Options for masking reference cryo-EM map: “all”, include everything; “threshold”, density value below the specified value will be masked out; “std”, density value below the specified standard deviations above the mean will be masked out.
Type: string
Default: threshold
Choices: [‘all’, ‘threshold’, ‘std’]
Masking Value for Simulated Cryo-EM Map (masking_level_traj): Input value for mask definition: for “threshold”, value below which to mask out, for “std”, standard deviation above mean below which to mask out.
Type: decimal
Default: 0.005
Masking Type for Cryo-EM Maps (masking_type): Options for how to combine the masks for trajectory and reference cryo-EM map: “union”, use the union mask from two maps; “overlap”, use the overlap mask between two maps; “reference”, use only the mask from reference map; “trajectory”, use only the masks from trajectory.
Type: string
Default: trajectory
Choices: [‘union’, ‘overlap’, ‘reference’, ‘trajectory’]
Selections for Output Best Structures
Superpose Control (superpose_ctrl): Toggle on to superpose trajectory onto input reference structure.
Required
Type: boolean
Default: True
Choices: [True, False]
Number of Top Candidates for Saving (ntop_out): Number of top candidates for each map to save to dataset.
Required
Type: integer
Default: 5
Output Best Structures for Input Cryo-EM Maps (struct_data_out): Output dataset saves the top N simulation structures for each input cryo-EM maps.
Required
Type: dataset_out
Default: best_structures_dataset
Selection Range for Trajectories
Start Iteration (first_iter): The start iteration of WE segments to be extracted. Leave empty to extract from the first iteration that is available.
Type: integer
End Iteration (last_iter): The end iteration of WE segments to be extracted. Leave empty to stop extracting at the last iteration that is available.
Type: integer
Endpoint Only (endpoint_only): By default, each WEMD segment has five conformers saved. If True, only the last one is used; if False, all five are used.
Required
Type: boolean
Default: True
Choices: [True, False]
Analysis Stride (N) (stride): Skip every N frames during analysis. No valid when the endpoint-only option is on.
Type: integer
Default: 1
Parameters for Estimating Free Energy Maps/Surfaces
Weight Free Energy Calculation (weight_option): Toggle on to apply WEMD weights when generating free energy maps (default=True).
Type: boolean
Default: True
Choices: [True, False]
Density Distribution Bins (number_bins): Number of bins for plotting density distribution in each dimension.
Type: integer
Default: 50
Maximum value of free energy (max_free_energy): Maximum value for showing estimated 2D free energy map in colors.
Type: decimal
Default: 50.0
Outputs for Cryo-EM Map Analysis
None (floe_report_name):
Type: string
Default: Failure Report
None (analysis_report_title): Title for the analysis report.
Type: string
Default: Cryo-EM Map Match Report
Output Features for Each WEMD Segment (analysis_data_out): Output dataset saves calculated features from all WEMD segments within selected ranges.
Required
Type: dataset_out
Default: output_features_dataset