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Model files contain structural information about substructures to be used in SEWING protocols. They are required for all SEWING movers.

Model files are generated using the SEWING Hasher application and can be filtered using the ModelTrimmer application.

Sample

#Model file created on 2015-9-24
#This model file contains of models from parent file ./giant_unwieldy_file.models
#All models with a segment containing dssp code(s) H have been removed
#Any model with helical (H) segment(s) fewer than 0 residues or greater than 1000 residues have been removed
#Any model with strand (E) segment(s) fewer than 18 residues or greater than 1000 residues have been removed
#Any model with loop (L) segment(s) fewer than 0 residues or greater than 5 residues have been removed

VERSION 1530590163
MODEL 80 6 11.9294 130.065 159.192 -27.0884 /Users/tjacobs2/PROJECTS/datasets/top8000/top8000_chains_70//1a2zFH_C.pdb
SEGMENT 7 E 1
RESIDUE 35 0 ALA -1
ATOM 1 17.602 46.603 -24.591
ATOM 2 16.364 46.555 -23.862
ATOM 3 15.398 47.642 -24.323
ATOM 4 15.74 48.774 -24.711
RESIDUE 36 0 MET 176.763 56.221 51.5357
ATOM 1 14.138 47.299 -24.189
ATOM 2 13.007 48.172 -24.336
...

Explanation

  • The top of the model file contains comments (printed by sewing_hasher or ModelTrimmer) indicating the date the file was generated and what input was used to generate it.
  • The VERSION line assigns a version number to each model file. This is used to ensure that SEWING edge files are only used with the SEWING model file from which they are generated. A model file and an edge file must have matching version numbers to be used together.
  • Each MODEL line has the following elements:
    • model_id: An integer used to identify the model
    • structure_id: An integer used to identify the structure from which the model was taken
    • distance
    • hoist_angle
    • packing_angle
    • meridian_angle
    • pdb_code: The PDB file from which the model was taken
  • Each SEGMENT line has the following elements:
    • segment ID: An integer used to identify the segment (unique within a model, but not between models)
    • Segment secondary structure (H, L, or E)
    • Should this segment be used for hashing? (1 or 0)
  • Each RESIDUE line has the following elements:
    • Residue number (w/respect to the starting structure)
    • Residue type
    • Chi angles
  • Each ATOM line has the following elements:
    • Element type (1, 2, 3, or 4). Only four backbone atoms (N, Calpha, C, and O) are stored.
    • x, y, and z coordinates

See Also