Utility

• Author: Rachel Seongeun Kim
• Table of Contents
  1. Tutorial
  2. ChimeraX Functions
     1. Foldseek Complex

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Tutorials

• ChimeraX tutorial(2023-12-01)

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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