#WARNING:no index is registered index 'YP_009725301.1' in 'http://www.uniprot.org/uniprot/' Modeling a 3D structure on 4yoj_A_1_F_1 by the Modeller program

Modeling a 3D structure on 4yoj_A_1_F_1 by the Modeller program (TEMPLATE: 4yoj)

If you install the Modeller program in your computer, you can model a full-atom 3D structure of the complex using following files.

Modeller scripts for complex

  1. Download modeller python script: model_complex.py

  2. Download alignment file: alignment_complex.ali

  3. Download template PDB file: 4yoj.pdb

  4. execute command:

    mod9 model_complex.py

Modeller scripts for each subunit

    Subunit 1

  1. Download modeller script: model1.py

  2. Download alignment: alignment1.ali

  3. Download template PDB file: 4yoj_A_1.pdb

  4. execute command:

    mod9 model1.py

    Subunit 2

  5. Download template PDB file: 4yoj_F_1.pdb

    Merge all the subunit models

  6. execute command:

    cat query1.B99990001.pdb 4yoj_F_1.pdb > model.pdb

Alignment for protein A:local for query, global for template[=>global both for query and template]