SSH connections for Mac OS 9

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.

SSH Programs for Mac OS 9

For systems running Mac OS 9.2 and below we are currently recommending a freeware program called NiftyTelnet (can be downloaded from here) and another freeware program called MacSSH (can be downloaded from here). There are currently two types of SSH running: version 1 (SSH1) and version 2 (SSH2). These two versions are NOT compatible. NiftyTelnet supports connections which use SSH1, and MacSSH supports SSH2 connections.

molbiol uses SSH2, with SSH1 support if people try to connect using programs that only understand SSH1. SSH2 is more secure. If your main reason for using an SSH program is to connect to molbiol, please use MacSSH. If you need to connect to other machines which run only SSH1, you may wish to choose NiftyTelnet so you can connect to machines running SSH1.

MacSSH for Mac OS 9

Basic Points about MacSSH

• easy to download and install
• supports SSH2 connections
• supports port forwarding
• looks and feels like a telnet session

Installing MacSSH
You can download MacSSH from the MacSSH web site. Choose the version that you need and click on the link. (The rest of these instructions will assume you have chosen MacSSH PPC, however the instructions should apply to the 68k version as well.). This should have created a folder on your desktop called MacSSH PPC. You can delete the accompanying MacSSH PPC.sit file. Move the MacSSH PPC folder to wherever on your machine you would like to store it.
That's it. You've installed MacSSH!

Configuring MacSSH

1. Open the folder and double click on the MacSSH PPC icon.
2. Under the File menu (at the top of your screen), click on Open Connection.
3. Type orac.molbiol.ox.ac.uk in the box under Host Name
4. Important: click on the box next to Secure Shell v2
5. Click on the Connect button.
6. You should now be prompted for your username and password. First time logins: If its the first time you have logged onto molbiol using MacSSH, you will be asked if you want to trust the host key. This means "do you believe that the machine that has answered your call to orac.molbiol.ox.ac.uk really is orac.molbiol.ox.ac.uk. Click on Accept and Save or Accept Once.
7. Once your username and password have been accepted, you should see a window that looks just like a telnet window. You can now work as you would usually.

Saving a session configuration in MacSSH
To speed things up, you can set up MacSSH so that you can choose a menu item and have a connection set up for you.

1. start up MacSSH by double clicking on the icon.
2. Go to the Favorites menu (at the top of your screen) and choose Edit Favorite.
3. Click on New in the window presented to you.
4. There are many options available to you under the tabs marked General, Network, Terminal, Security, OTP, SSH2 and Firewall. Feel free to peruse all the options, but please set the ones we mention explicitly here:
5. Under the General tab:
   • type in a name for your session in the box labeled Alias
   • in the box called Hostname, type orac.molbiol.ox.ac.uk
   • click on the arrow key next to the box labeled Port and select SSH from the choices offered. This will change the number in the box next to Port to 22
6. Click on the Security tab:
   • Click on the drop down menu next to the word Protocol (by default, this is set to telnet)
   • Choose ssh2 (secure shell).
7. Click on OK (in the Edit Favorites window).
8. Click on OK (in the Favorites window).

Now click on the Favorites menu (at the top of your screen). You should see the name of the session you just created. If you choose this option, you should be prompted for your username and password directly.

NiftyTelnet for Mac OS 9

Basic Points about NiftyTelnet

• easy to download and install
• supports only SSH1 connections
• looks and feels like a telnet session
• scp, a secure way of copying files between your account and your local computer, is included and easy to use.

Installing NiftyTelnet
You can download NiftyTelnet from the NiftyTelnet web site. Click on the link in the Software Download Box on the NiftyTelnet site. A file folder called niftytelnet-1.1-ssh-r3 folder (please note that the version number you are downloading may be different) should appear on your desktop. Move this folder to wherever you wish to store it. You can delete the accompanying file called niftytelnet-1.1-ssh-r3.sit
That's it. You've installed NiftyTelnet!

Configuring NiftyTelnet

1. Open the niftytelnet folder. When you get time, please read the README SSH file.
2. Double click on the NiftyTelnet icon (which looks like a large N).
3. Click on New Connection under the File menu (at the top of your screen).
4. Type orac.molbiol.ox.ac.uk in the box labelled Hostname, and click on Connect. You should then be prompted for your username and password. First time logins: If its the first time you have logged onto molbiol using NiftyTelnet, you will be asked if you want to trust the host key. This means "do you really believe that the machine that has answered your call to orac.molbiol.ox.ac.uk really is orac.molbiol.ox.ac.uk. Click on Accept and Save or Accept Once.
5. After your username and password have been accepted, you should be logged in, with a window that looks just like a telnet window.

Saving a session configuration in NiftyTelnet
To speed things up, you can set up NiftyTelnet so that you can choose a menu item and have a connection set up for you.

1. Click on New Connection under the File menu.
2. Click on the New button in the window presented.
3. Type a name for your session in the Shortcut Name box.
4. Type your username in the appropriate box.
5. Set the protocol to SSH-3DES using the pull down menu.
6. Click on OK.

You should now find your shortcut name listed in the Shortcuts section of the window. If you click on this name and then click on the Connect button, you should be prompted for your password.

MacSFTP for Mac OS 9

For systems running Mac OS 9.2 and below we are currently recommending a program called MacSFTP. This is shareware software and will work for 15 days before requiring a serial number, which can be purchased online here. The current cost of the shareware license is £15.00. Information about the software can be found at: here.

Making the Connection to Molbiol using MacSFTP

1. When you have downloaded the software you will have a folder called MacSFTP Classic on your system. Open the folder and double-click on the MacSFTP Classic icon to run the program. The following message will be displayed:

2. Click the OK button. The SFTP login screen will then be displayed:

3. Enter host name as above and your username and password.
4. Click on the Connect button, the following message will only be displayed the first time you connect to molbiol using MacSFTP:

5. Click on the Yes button to continue connecting to molbiol. You will then see a window listing the files you have stored on your molbiol account:

File/Quit is used from the menu bar to break the connection to molbiol and exit the application.

Bookmarking your Molbiol, Settings

1. In order to ensure you do not have to type in all your details every time you use MacSFTP you can create a bookmark to molbiol. To create the bookmark select Bookmarks, New Bookmark from the menubar:

2. You will be prompted to enter a password

3. Enter a password and click on the OK button. You will then get the following prompt:

4. Enter the password you decided on and click OK. The screen will then display a window with the setting you entered initially to connect to molbiol:

5. Enter an appropriate name in the Name field such as molbiol and click the Save button. You will be prompted to enter your pass phrase again in order to confirm the bookmark save.

To use your bookmark in the future, double click on the MacSFTP Classic icon to run the program. Click the Cancel button when the SFTP login screen is displayed. Go to Bookmarks on the menu bar, scroll down to molbiol and select it. You will be prompted to supply your Bookmarks pass phrase, enter your password and click OK the connection will then be made to molbiol.

Transferring Files using MacSFTP
Having connected to molbiol and with the window displaying a list of your files:

In order to transfer files to-and-from your molbiol account it is simply a question of clicking and dragging the files you wish to transfer from one window to the another. Open a window on your Macintosh to display the files you wish to transfer, click on the file's icon and drag it to the SFTP molbiol window. The dragged files will be copied on to your molbiol account. To transfer from molbiol to your Macintosh drag the file from the SFTP molbiol window to the Macintosh.

If you are moving Macintosh binary files (such as application programs) on to your molbiol account and wish them to be re-useable on the Macintosh when you transfer them back from molbiol to the Macintosh you need to change your MacSFTP settings preferences. Go to Edit then Preferences on the menu bar then click on the File Transfer tab:

Click on the Upload files using MacBinary checkbox and ensure that there is a tick on the only when needed checkbox. This will ensure that Macintosh binary files are correctly transferred to-and-from your molbiol account. Click on the Save button.

File/Quit is used from the menu bar to break the connection to molbiol and exit the application.

Guide to configuring eXodus to contact molbiol

If you would like to use software with a graphical user interface (GUI), such as clustalX, seqlab, or staden, you first need to install a program that allows you to run the X window graphical displays on your Mac. Please note: the secure SSH connection between your machine and the server, orac, will be handled by MacSSH (see above) - eXodus is only used to display graphics once the connection is made.

Absolute requirements: You must have an ethernet connection, an IP address and MacTCP or Open Transport, at least 6 MB of RAM over and above the system requirements (which may be virtual memory) and preferably a PowerPC processor.

eXodus version 8 is now available. It is not available from the OUCS shop, but can be obtained from a company called Edas. They do have academic discounts.

Configuration: At many points during this configuration procedure, eXodus may ask to reset itself. Just say yes.....

1. Install eXodus. You should do this with the normal default install.
2. Highlight the eXodus icon by clicking on it once. Go to Finders Get Info box (found under File pulldown menu) and allocate eXodus at least 8MB of memory, more if you have it (12 if you want to run AceDB). Close this window and then start eXodus.
3. From the Settings pull-down menu select Server Settings. Click on the Screen icon on the left and set the Type (on the right) to be rootless Macintosh.
4. Some software, for example Dotter and Lalign, only work if you choose to display 256 colors. To set this, go to Settings and choose Server Settings. In here, click on Screens, and then on the option Advanced settings. In here, click on Colors and choose 256 colors.
Click Save and close the window.

In addition you will need to set the DISPLAY environment variable.

1. Open a terminal and log on to orac (see the section on MacSSH)
2. To set the DISPLAY variable, molbiol users can simply use the command, mydisplay
3. logout

You have now completed the setup of eXodus for use with a secure SSH connection to orac. Once you have restarted eXodus and logged back on to orac, you can quickly test the graphical X-display by typing xclock. You should see a clock dial displaying the current time.