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Frequently Asked Questions

  1. How do I download ConSurf-DB results?

  2. ConSurf-DB is a file based database.
    The rsync command is used to download a single entry or the entire database to your local location.

    To download a single entry please use the following command:
       rsync -av<PDB ID>/<Chain ID> <your local target directory>
    To download the entire database (can take several hours) please use the following command:
       rsync -av <your local target directory>

    Please note:
    • The database contains more than 55,000 sub-directories; make sure your file system supports that amount of sub-directories before attempting to download the entire database.
    • If you only need to download a few results please use the web interface as explained below
    • Both PDB ID and Chain ID directory names must be in capitals.

  3. Can I obtain only part of ConSurf-DB results according to a list of structures I have?

  4. Yes you can!
    You may upload a file to the server (using the third option in the main page, 'Upload a list of PDB files') which details all the PDBs or PDBs/chains you are interested in. The server will zip all of the files in one folder, which you will be able to download.
    Please note! The entries in the file should be written in either one of these 3 formats:
    • <PDB ID>
    • <PDB ID>_<CHAIN>
    • <PDB ID>/<CHAIN>
    Each entry should be separated from the previous one with a new line character!
    Please see the attached file for an input example.
    Please see the attached file for a zipped output example.

  5. How do I create my own copy of ConSurf-DB?

  6. Please read further instructions and download the code, using the source page.