Installing Cygwin

Go to cygwin.com, click on the "Install Cygwin now" web installer. Select a fast mirror site, and follow the default options until you come to the "Select Packages" window. If you have reasonable disk space, just click on the word "Default" of the "+All Default" top item, to make it "+All Install". This will install all packages available. If you do have disk space limitation, you should set subcategories "+Net Install", "+Shells Install", and "+X11 Install", while select other packages as "Default". You can always come back and install more packages.
After everything is finished, in Windows, copy c:\cygwin\usr\X11R6\bin\startxwin.bat to c:\cygwin\startxwin.bat. Right click on c:\cygwin\startxwin.bat and click on "Edit". This will open up Notepad. Go to almost the end of the file, you will find a line:
```
run xterm -e /usr/bin/bash -l
```
I like to run tcsh as my login shell, so I change it to:
```
REM run xterm -e /usr/bin/bash -l
run xterm -e /usr/bin/tcsh -l
run xhost +
```
The last line "xhost +" allows any X client to connect to the cygwin X server, including those on remote machines. Save the changes by pressing "Ctrl+s" and quit Notepad. Then right click on c:\cygwin\startxwin.bat again, this time "Send To" -> "Desktop (create shortcut)". You will find an icon "Shortcut to startxwin.bat" on your desktop. I usually do three more things to beautify it: (a) rename the desktop icon to just "startxwin", (b) right click on the desktop icon, go to "Properties", and in the "Shortcut" tab, change "Run: Normal window" to "Run: Minimized", (c) in the same "Shortcut" tab, click on "Change Icon..." -> "Browse...", and go to c:\cygwin directory, and select the distinctive green&black banner.
Now if you click on the desktop icon, you should get an X-Window terminal, running tcsh. If it works, close the terminal window and go to the next step.
Download and save the dot files .cshrc, .Xdefaults, .emacs to your "~/" directory, likely some directory called "c:\cygwin\home\username\". Windows may rename the file .cshrc to .cshrc.txt, in which case you need to rename them back
```
mv .cshrc.txt .cshrc
mv .Xdefaults.txt .Xdefaults
mv .emacs.txt .emacs
```
inside cygwin.
Alternatively, you may use wget to download the files directly inside cygwin, if you have already installed wget.
Now if you click on the desktop icon, you should see a gray X terminal with yellow cursor.
Download and save Co.tar.gz to your "~/" directory. Run in the previous X terminal,
```
% tar xvfz Co.tar.gz
```
You will get a bunch of shell scripts, a lot of customization for Emacs, LaTeX, etc, and some binaries like AtomEye. Try it out:
```
% rehash
% A Co/Runtime/Rasmol/PDB/Nanotube8x3x1.cfg
```
For those with port 22 open to the outside and can run sshd, you can set up a VNC server.
To access a VNC server (say on mse-jl1.eng.ohio-state.edu), you need to run
```
% ssh -L5901:mse-jl1.eng.ohio-state.edu:5901 -X lij@mse-jl1.eng.ohio-state.edu
```
in your cygwin terminal to tie up mse-jl1.eng.ohio-state.edu:5901 with local port 5901 through ssh encryption. You can then (a) install Windows VNC client program, (b) run it, click on "Options...": in the "Misc" tab, select "Shared connection (do not disconnect other viewers)"; and finally in the "Load/Save" tab, click on Defaults "Save" to save these options. (c) connect to server "localhost:1" (which is L5901), click "OK", type in the VNC password, and viola! The next time you connect, you only need to do (c) since the options are saved.
To automate login to VNC server, edit c:\cygwin\cygwin.bat, and change bash --login -i to tcsh -l.
Then click on c:\cygwin\cygwin.bat to log in, and in tcsh prompt:
```
tunnel atom.mit.edu vnc
```
to enable password-less ssh login to atom.mit.edu.
Then,
```
cp /cygdrive/c/Program\ Files/RealVNC/VNC4/vncviewer.exe /bin
```
so vncviewer can be invoked in tcsh command line.
Edit /cygdrive/c/cygwin/atom-5.bat
```
@echo off
C:
chdir C:\cygwin\bin
tcsh -c "/bin/vncviewer &; ssh -L5905:atom.mit.edu:5901 vnc@atom.mit.edu"
```
The Windows vncviewer application window should pop up as you click on atom-5.bat. Fill in "localhost:5905" in the vnc window.
For concurrent voice communication, set up Skype. We recommend a headset like this. The list of our group's Skype usernames is kept here.

Email: li.562@osu.edu, phone: 614-292-9743.