HOMCOS : Searching and Modeling of 3D Structures of Complexes

How to use MODELLER
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The HOMCOS server only provides template structures and "sequence-replaced model", we recommend to use the Modeller to model more detailed full atomic models,. This help page explains how to execute the Modeller program using files provided by the HOMCOS server. We explain the Windows 10 environment, however, you can use it also in Mac and Linux environments. The installing is explained in another help page.
  1. Preparation of files for Modeller

    The 3D model view services from all the HOMCOS services provide files for Modeller. As an example, this help page uses modeling Hetero protein multimer .

    1. Access the page hetero multimer modeing、input CDK5_HUMAN and CCNB1_HUMAN as queries.
    2. A following result will be shown. Click the PDB code 2jgz in the first row.

      [show WEB page]
    3. A following 3D model view will be shown.

      [show WEB page]
    4. Click the icon [Modellar script]. A following page will be displayed.

      [show WEB page]
    5. Download three files into your computer:"model_complex.py", "alignment_complex.ali", and a template PDB file("2jgz.pdb"). This help page assumes that you are using Windows 10 PC with the account name visitor and downloading your own "Downloads" directory, such as C:\Users\visitor_en\Downloads.

  2. Execute Modeller by your own PC

    Wi will explain the case for Windows 10. Your PC has to have the Modeller program. If not, install it by the help page for install.

    1. Push the start button , and choose [All apps].

    2. From the category "M", choose the folder [Moderller9.17], and choose the command prompt [Modeller].

    3. A following command prompt for Modeller will be displayed. This command prompat already has the Modeler envieonmental variables.

    4. Move to the directory where you downloaded the three files of Modeller from the HOMCOS server. If the folder is C:/Users/visitor_en/Downloads, type a following command in the command prompt:
      cd C:/Users/visitor_en/Downloads or
      The command cd is for change directory.

    5. Type the command dir to confirm the required three files.
      dir or
      If you are in the correct directory, you can see three files: model_complex.py, alignment_complex.ali, a template PDB file (2jgz.pdb).

    6. Type a following command to execute Modeller:
      mod9.17 model_complex.py or
      Wait a while, it takes a few minutes to finish.

    7. After finishing the calculation, type again the command dir to confirm output files.
      dir or 
      The file with 、.B99990001.pdbis a PDB file for a modeled structure. In this case, the file model_complex.B99990001.pdb is the file for model 3D structure.

    8. Confirm the modeled structure (.B99990001.pdb) using the srandard molecular viewer, such as UCSF Chimera or PyMOL.

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