SSH connections for Mac OS X

In order to use your molbiol account we recommend a program that creates a secure (SSH) connection to the molbiol server, "orac". This connection will encrypt traffic between the server and your computer - including your password. It will help to protect all molbiol account holders by preventing username and password "sniffing" on the internet.

It is no longer possible to transfer files between a local machine and the server using FTP. Instead, you can make use of the secure SSH connection to transfer files using SFTP.

Connections to molbiol - Mac OS X 10.3

Although it is possible to connect to molbiol using the simple terminal application (Applications/Utilities/Terminal) we recommend using the x-term for all connections. This will allow you to gain maximum use of the software available via your molbiol account.

Before you use the x-term you must ensure that Apple's X11 for Mac OS X 10.3 has been installed and configured on your machine. This software is available as an optional installation when you install Mac OS X 10.3 (Panther), meaning that the Panther installer does not automatically install Apple's X11 1.0. You need to click "Custom" in the Easy install pane then select X11. If you forgot to select it while installing Panther, you can install it later by opening (double clicking) the X11User.pkg file which you can download in compressed form here or from the Apple website. Further details regarding X11 for Mac OS X can be found at the Apple website.

Use the following set of instructions to install and configure X11 for Mac OS X 10.3:

Double click on the X11User.pkg icon to open the installer (Fig 1).

When prompted for a destination (Fig 3), click on HD and click continue

When prompted for an installation type (Fig 4), click upgrade

Using X11 - logging in from Mac OS X 10.3

You have to specifically enable X11 by adding "-X" when logging in. To log in to molbiol you would do the following:

• Start X11 (from "Applications" and then "Utilities")

• Within X11, open a new xterm window by choosing "Applications" and then "Terminal".

• To connect to molbiol type the following and press the return key:
  (Note: in the example below, the -X is upper-case, and the -l is a lower-case 'L' )
  ssh -X -l username orac.molbiol.ox.ac.uk

Connections to molbiol - Mac OS X 10.4

Although it is possible to connect to molbiol using the simple terminal application (Applications/Utilities/Terminal) we recommend using the x-term for all connections. This will allow you to gain maximum use of the software available via your molbiol account.

Before you use the x-term you must ensure that Apple's X11 has been installed and configured on your machine. X11 can be installed on your Mac OS X 10.4 machine using the Tiger DVD installer disk. Further details regarding X11 for Mac OS X can be found at the Apple website (and on the Apple developers site.

Using X11 - logging in from Mac OS X 10.4

You have to specifically enable X11 by adding "-Y" when logging in. To log in to molbiol you would do the following:

• Start X11 (from "Applications" and then "Utilities")

• Within X11, open a new xterm window by choosing "Applications" and then "Terminal".

• To connect to molbiol, type the following and press the return key:
  (Note: in the example below, the -l is a lower-case 'L' )
  ssh -Y -l username orac.molbiol.ox.ac.uk

Fugu (SFTP and SCP) on OS X

Fugu (which can be freely downloaded from The Research Systems Unix Group at the University of Michigan) can be used to provide a Graphical User Interface (GUI) to the SFTP command. Having downloaded the Fugu application, copy the Fugu file into the Applications folder - then drag the icon to the Dock so that you have the application easily accessible.

Click on the Fugu icon in the Dock to run the program. This will display a window listing the files in your current working directory (/Users/your_account):

Enter the connection details for molbiol as shown below (giving your molbiol account name), click the Add to favourites button to add these settings to your Favourites list, then click Connect:

The following message will then be displayed:

This message is only displayed the first time you connect to a site. Click Continue. You will then be prompted for your molbiol password:

Enter your password and click Authenticate. The connection to molbiol will then be established and a window will open displaying your molbiol files:

To transfer files simply drag-and-drop between windows.

Use Fugu/Quit Fugu on the menu bar to exit the software.

Command Line SFTP on Mac OS X

SFTP comes as standard on Mac OS X systems and can be accessed via the command line from the x-term (see above). Access to molbiol can be achieved via the command line command (It is necessary to press the Return key after entering each command.):
sftp login_name@orac.molbiol.ox.ac.uk

SFTP commands:

• help to display a list of available commands. The default directory on the Macintosh will be the top level of your user account /home/your_group/your_account.
• lls can be used to list the contents of the local (Macintosh directory).
• lpwd will print the local directory.
• pwd prints the remote (molbiol) directory.
• put is used to upload a file from the Macintosh to molbiol, for example:
  put local_filename molbiol_filename
• get is used to transfer files from molbiol to the Macintosh, for example:
  get molbiol_filename local_filename



• Type bye to exit.