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Installation of the VMBiskit virtual machine.
  1. Download and install the free VMWare Server from:

  2. Download the vmbiskit snapshot from

  3. Unpack the snapshot

    • On Unix:

      tar jvfx vmbiskit_ubuntuserver.tar.bz2
    • On Windows: 7-Zip ( allows to unpack bz2 under Windows.

      (Thanks to Anders Norgaard for this hint!)

  4. Open the virtual machine in VMWare

    • File / Open / Browse -> vmbiskit_ubuntuserver/
    • Start (Note: Reply 'Keep' when asked about changing the hardware ID)
    • login with user name biskit and password biskit
  5. Connect to the virtual machine

    The vmbiskit snapshot is a text-only installation but it can 'forward' graphical x11 windows to your host computer. The system is configured to fetch a dynamic IP address from DHCP (modify these settings in /etc/network/interfaces). To access it from outside, you need to know which IP address was assigned to it.

    • on vmbiskit: read the IP address with ifconfig:

      vmbiskit|~> ifconfig
      eth0      Link encap:Ethernet  HWaddr 00:0C:29:4F:52:46
                inet addr:  Bcast:  Mask:
                inet6 addr: fe80::20c:29ff:fe4f:5246/64 Scope:Link
    • Note the address given after 'inet addr:'

    • Now connect to the vmbiskit machine from your host:

      ssh biskit@

      Replace '' with the address noted above.

      And check that you can open graphical windows:

      vmbiskit~> pymol

      If pymol doesn't open, try to re-connect with 'ssh -X biskit@'

  6. Bring everything up-to-date

    • upgrade to the latest biskit version:

      cd ~/py/biskit
      svn update

    See also: Update VMBiskit


No network connection

If 'ifconfig' does not report any but the loopback IP, Ubuntu may have become confused by the changing hardware address (a consequence of moving the VMWare snapshot between different computers).


  • Edit /etc/udev/rules.d/70-persistent-net.rules: remove any non-comment line
  • Edit /etc/iftab: remove any non-comment line (if any)
  • reboot [sudo reboot] (restarting the network is not enough)

apt-get doesn't work

Installation of other software packages may require the Ubuntu CD. -> uncomment the cd repository in /etc/apt/sources.list or Download the Ubuntu 7.10 server edition CD image (32 bit x86) and mount it into the virtual CD-drive. See: VMWare / VM / Settings -> CD-drive