#WARNING:no index is registered index 'YP_009725295.1' in 'http://www.uniprot.org/uniprot/' Modeling a 3D structure on 3snd_A_1_B_1_C_1_D_1_E_1 by the Modeller program

Modeling a 3D structure on 3snd_A_1_B_1_C_1_D_1_E_1 by the Modeller program (TEMPLATE: 3snd) 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: model_complex.py

  2. Download alignment file: alignment_complex.ali

  3. Download template PDB file: 3snd.pdb

  4. execute command:

    mod9 model_complex.py

Modeller scripts for each subunit

    Subunit 1

  1. Download template PDB file: 3snd_A_1.pdb

    Subunit 2

  2. Download modeller script: model2.py

  3. Download alignment: alignment2.ali

  4. Download template PDB file: 3snd_B_1.pdb

  5. execute command:

    mod9 model2.py

    Subunit 3

  6. Download template PDB file: 3snd_C_1.pdb

    Subunit 4

  7. Download template PDB file: 3snd_D_1.pdb

    Subunit 5

  8. Download template PDB file: 3snd_E_1.pdb

    Merge all the subunit models

  9. execute command:

    cat 3snd_A_1.pdb query2.B99990001.pdb 3snd_C_1.pdb 3snd_D_1.pdb 3snd_E_1.pdb > model.pdb

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