X windows on tak or hebrides

Using X windows on tak or hebrides

Connecting the first time with VNC | Connecting subsequent times with VNC | Connecting with eXodus | Applications | Help

To use X Windows on tak or hebrides, Mac users can choose between two systems, VNC (a free product) and eXodus. PC users can use the VNC system.

Connecting the first time with VNC:

Download a VNC viewer file for Windows, Macintosh (from VNCThing), or another OS to anywhere on your desktop computer. If you're on a Mac, unpack the file with Stuffit (if it doesn't unpack itself).
Use the secure shell to connect to tak as usual. If you've never done this before, download "MacSSH PPC" (for Macs) from Enigma (Applications > Misc. tools > MacSSH PPC > MacSSH PPC) or download SSHWinClient from SSH (for Windows). The file will look like SSHSecureShellClient-?.?.?.exe
After logging in to tak, issue the following command: vncserver
Since this is the first time for running this command, you will be asked to select a password (that can be changed later with this command: vncpasswd). This password need not be (but can be) the same as your tak login password.
A second time, issue the following command: vncserver

Read the message you get back; it should be something like

	New 'X' desktop is tak:18

	Creating default startup script /home/your_user_name/.vnc/xstartup
	Starting applications specified in /home/your_user_name/.vnc/xstartup
	Log file is /home/your_user_name/.vnc/tak:18.log

Go to wherever you put the viewer application on your desktop and click to run it.
When the window pops up, type in
```
tak.wi.mit.edu:n
```
where "n" is number you received after running 'vncserver' (18 in the example above)
After entering the appropriate number, i.e.,

click "OK" and enter the password you just chose.
The X windows screen should pop up on your desktop ==> you're ready to go.
See below for some applications that take advantage of the graphical interface
Closing your desktop window doesn't terminate the session. Just reconnect by clicking on the viewer on your desktop and entering the session details.
To permanently end this session, enter the command
```
vncserver -kill :n
```
(where "n" is the number of the session [18 in the above example])

Connecting subsequent times with VNC:

Use the secure shell to connect to tak as usual.
After logging in to tak, issue the following command: vncserver

Read the message you get back; it should be something like

	New 'X' desktop is tak:18

	Creating default startup script /home/your_user_name/.vnc/xstartup
	Starting applications specified in /home/your_user_name/.vnc/xstartup
	Log file is /home/your_user_name/.vnc/tak:18.log

Go to wherever you put the viewer application on your desktop and click to run it.
When the window pops up, type in
```
tak.wi.mit.edu:n
```
where "n" is number you received after running 'vncserver' (18 in the example above)
After entering the appropriate number, i.e.,

click "OK" and enter your x windows password.
The X windows screen should pop up on your desktop ==> you're ready to go.
See below for some applications that take advantage of the graphical interface
Closing your desktop window doesn't terminate the session. Just reconnect by clicking on the viewer on your desktop and entering the session details.
To permanently end the session, enter the command
```
vncserver -kill :n 
```
(where "n" is the number of the session [18 in the above example])

Connecting on a Mac with eXodus:

Download the MacSSH_PPC folder from the Applications volume of Enigma.
Run eXodus (double-click on the icon) but do NOT use it to open a session.
Run the ssh application (in the folder you downloaded from Enigma) and use it to login to tak using your username and password.
In the ssh window, find out the hostname of the machine you are connecting to tak from by running the command 'who' and locating your username and current session in the list.
In the ssh window, type the command:
```
setenv DISPLAY hostname.wi.mit.edu:0
```
replacing 'hostname' with the hostname you found from the 'who' command
To move files between the Macintosh and tak - from the Macintosh select AppleShare and the Ethernet zone. Then choose tak from the Select a file server box. Type in your tak login name and password and click okay. Your tak volume is now mounted.

Some applications:

To get a menu with many of these applications customized for tak, place the file twmrc into your home directory and rename it to .twmrc The next time you start X windows, it'll take effect.

command	application
xterm	classic command window
xterm3d	like xterm but more 3d
xemacs	xemacs (good text editor)
xemacs -bg black -fg white	open xemacs with custom colors
clustalx	multiple sequence alignment tool
jalview	multiple sequence alignment editing tool (ex: jalview mySeqs.fa FASTA)
matlab	Matlab package (help)
phoenix	web browser
setenv DISPLAY unix:foo.0	set display if needed
who -m	get name of display
xclipboard	Clipboard (to help with copying and pasting)
clock	an analog clock
xclock -d	a digital clock
xcalc	calculator
xload	see how hard tak is working
xman	unix (man) help pages
display	view an image (ex: display picture.jpg)
xeyes	eyes that follow your mouse
echo $DISPLAY	Get your display for this session

Help:

Your mouse must be over a window to use the keyboard in that window.

Use the upper right hand icon in most windows to resize them. They must be made larger before they can be made smaller.

To close a window with no pull-down menu, double click anywhere but on a window, place the cursor over the window to close, and use the left mouse button.

If you placed the .twmrc file in your home directory, click on the background with the left mouse button to get a menu of some applications. Note that "Applications" leads to GCG, Matlab, and SAS. Clicking on the background with the right mouse button opens another menu. One of the choices, "Show Iconmgr", may be helpful to stay organized if lots of windows are open at once.

If copying and pasting doesn't seem to work, use the clipboard (command: xlipboard &)

Going from X windows to desktop:
- Select text to be copied using the left mouse button and use 'copy' from the pull-down menu.
- Copied text should appear on the clipboard.
- Select text from clipboard and hit ENTER.
- Paste text into your desktop application.
Going from desktop to X windows:
- Select and copy text as usual.
- While mouse is on a new clipboard, hit both mouse buttons at once.
- Paste text into X windows application.

Problem: For some applications, you may receive an error message such as

	Xlib: Client is not authorized to connect to Server

	SeqLab cannot open your display.
	Please do a setenv DISPLAY ... and try again.
	Make sure your display authorizes connections from your host.
	Consult your system manager for help.

Solution: issue the command

	setenv DISPLAY unix:n.0

where "n" is the number for your specific connection (18 in the example above).

For thorough help about connecting, see the online documentation for Virtual Network Computing