Rosetta@home

How to view your structure predictions.

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By following the instructions below, you can view your protein structure predictions using a freely available molecular viewing program.


  1. First find the result file of the Rosetta@home work unit in progress whose structures you want to view.

    Result files have a ".out" file extension and reside in BOINC core client slot sub-directories which are named 0, 1, ... N-1 and located in the "slots" directory. There should be one ".out" file in each slot sub-directory of Rosetta@home work units in progress.

    The default locations of slot sub-directories are the following:

    • Windows: C:\Program Files\BOINC\slots\
    • Linux: $home/BOINC/slots/
    • Mac: /Library/Application Support/BOINC Data/slots/

      For information about the BOINC core client file structure, click here.
  2. Copy the result file to the Rosetta@home project directory (do not move or modify the original file).

    The default locations for the Rosetta@home project directory are the following:

    • Windows: C:\Program Files\BOINC\projects\boinc.bakerlab.org_rosetta\
    • Linux: $home/BOINC/projects/boinc.bakerlab.org_rosetta/
    • Mac: /Library/Application Support/BOINC Data/projects/boinc.bakerlab.org_rosetta/
  3. Extract the protein structure predictions from the ".out" result file using Rosetta.

    Rosetta saves each prediction in the ".out" file using a special condensed format to help reduce bandwidth. In order to view the structures using a molecular viewing program, you have to extract them from the result file using a standard file format (PDB) that the viewing program can read. You can do this by running Rosetta with one of the special commands as described below. The correct command to use will depend on the work unit. To determine the correct command, try all commands using the instructions below until you successfully extracted the structures by getting the expected output ".pdb" files.

    Rosetta commands:

    1. ROSETTA -extract -all -s XXXXXX.out
    2. ROSETTA -extract -all -fa_input -s XXXXXX.out

    ("ROSETTA" should be replaced with the Rosetta executable and "XXXXXX.out" should be replaced with your ".out" result file)

    • For Windows:

      1. Using a text editor, create a ".bat" batch file that contains the first command line above where "ROSETTA" is replaced with the Rosetta executable and "XXXXXX.out" is replaced with your ".out" result file. The Rosetta executable should be located in the Rosetta@home project directory. Save the ".bat" file in the Rosetta@home project directory. You can give it any unique name but keep the .bat file extension. If you are familiar with running commands using the command prompt, you can skip the batch file by opening a command prompt window, going to the Rosetta@home project directory, and running the command.
      2. Execute the ".bat" file by double clicking it. (note: the batch file, Rosetta executable, and result file have to be located in the Rosetta@home project directory)
      3. Make sure ".pdb" files exist in the Rosetta@home project directory with file names that follow the format: S_XXXX_XXXX.pdb or F_XXXX_XXXX.pdb where the X's are numbers. If they do not exist. Try the next command line above.


    • For Linux and Mac:

      1. Open a terminal window, go to the Rosetta@home project directory, and run the command above where "ROSETTA" is replaced with the Rosetta executable (located in the Rosetta@home project directory) and XXXXXX.out is replaced with the name of your ".out" result file. (note: the Rosetta executable and result file have to be located in the Rosetta@home project directory)
      2. Make sure ".pdb" files exist in the Rosetta@home project directory with file names that follow the format: S_XXXX_XXXX.pdb or F_XXXX_XXXX.pdb where the X's are numbers. If they do not exist. Try the next command line above.

    By running the Rosetta command, your structure predictions will be saved in the Rosetta@home project directory as ".pdb" files which can be viewed using a molecular viewing program. The number of ".pdb" files will depend on the number of structure predictions that have been made so far for the particular work unit.

  4. View your extracted PDB files using a molecular viewing program.

    There are a number of molecular viewing programs that are available online for free.

    If you are not familiar with molecular viewing programs, we recommend using Rasmol. A Quick Start guide is available at http://www.umass.edu/microbio/rasmol/rasquick.htm.

  5. Clean up the Rosetta@home project directory by removing the newly generated ".pdb" files whose names have the format: S_XXXX_XXXX.pdb where the X's are numbers. Be careful not to remove other files in the directory. Alternatively, you can move the ".pdb" files to another directory that is not located in your BOINC client installation directory.

    This step is optional but keep in mind that the extracted structures will take up the disk space allotted for Rosetta@home.




Please send comments and suggestions to dekim at u.washington.edu


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Last Modified: 4 May 2011 23:09:16 UTC
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