Modeling a 3D structure on 2jdq_A_1_B_1_C_1_D_1 by the Modeller program (TEMPLATE: 2jdq) assembly_id:1)

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:

  2. Download alignment file: alignment_complex.ali

  3. Download template PDB file: 2jdq.pdb

  4. execute command:


Modeller scripts for each subunit

    Subunit 1

  1. Download template PDB file: 2jdq_A_1.pdb

    Subunit 2

  2. Download modeller script:

  3. Download alignment: alignment2.ali

  4. Download template PDB file: 2jdq_B_1.pdb

  5. execute command:


    Subunit 3

  6. Download template PDB file: 2jdq_C_1.pdb

    Subunit 4

  7. Download template PDB file: 2jdq_D_1.pdb

    Merge all the subunit models

  8. execute command:

    cat 2jdq_A_1.pdb query2.B99990001.pdb 2jdq_C_1.pdb 2jdq_D_1.pdb > model.pdb

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