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Utility

Tutorials

ChimeraX

Functions specialized for Foldseek Complex

Helper functions to visualize the result of complexsearch and complexcluster source code
example data

  1. Functions

    • rotate_translate : rotate and translate the complex by providing the ut matrix
    • superpose_complex : open query and target, and superpose the complex by providing scorecomplex report file
    • show_cluster : open all pdb files in the cluster, and superpose members on the representative by providing scorecomplex report file and complexcluster result file
    • print_tmscore : print the TM-score of the complex by providing scorecomplex report file, query and target
    • print_ut : print the UT matrix of the complex by providing scorecomplex report file, query and target
    • print_report : print the report of the complex by providing scorecomplex report file, query and target

  2. Features

    • cluster alias : use the cluster as a unit e.g. show specific cluster (clu_repname)

  3. How to use

    open visualize_foldseek_complex.py

# 1. rotate_translate
open query.pdb
open target.pdb
rotate_translate #2 0.001,0.002,0.003,0.004,0.005,0.006,0.007,0.008,0.009,100,200,300

# 2. superpose_complex
superpose_complex /path/to/scorecomplex_report query,target pdb_path /path/to/pdb_dir qt_id 1,2

# 3. show_cluster
show_cluster /path/to/scorecomplex_report /path/to/complexcluster_result pdb_path /path/to/pdb

# 4. print functions
print_tmscore /path/to/scorecomplex_report query,target
print_ut /path/to/scorecomplex_report query,target
print_report /path/to/scorecomplex_report query,target

----------
## Additional information
# 1. cluster alias e.g. clu_7soy_1
hide cartoon
show clu_7soy_1 cartoon

  4. Visualized examples from ChimeraX
    show_cluster

    show clu_7soy_1 cartoon

    superpose_complex