Other software
Queen's University Protein Function Discovery
and Department of Biomedical and Molecular Sciences
Molecular Modelling and Crystallographic Computing Facility
Crystallography and Modelling:

Other software

If no manual link is present in this list of software and you are not sure how to proceed with a program, try man program_name for more information or try program_name -h for help if man program_name does not work. If you don't know the name of a program, but are looking for help to do a particular task, try apropos keyword or man -k keyword (really the same thing).

SSH software

To allow you to connect to our Linux computers via ssh, you need an program on your Windows or Macintosh computer. The following programs can be copied from the /prog/win and /prog/mac directories to your PC or Mac.
  1. putty for Microsoft Windows
  2. WinSCP open source SFTP (SSH File Transfer Protocol) and SCP (Secure CoPy) client for Windows
  3. Tera Term Pro from Queen's Packman
  4. nifty telnet for Apple Macintosh, available from Queen's Macintosh Software Manager

Virtual Network Computing

To allow X-window access from windows computers to our Linux computers, or use your Windows-based computer at home to access your Windows-based computer at work.
  1. RealVNC (free download and open source)

Mail software

  1. mutt the best (in my not so humble opinion!) of the cursor-based, menu-driven e-mail programs, similar in appearance to elm but with many improvements making it much more powerful.
  2. elm menu-driven but cursor-based program, much easier than the above. "Cursor-based" means that it can run on any terminal.
  3. pine simple menu-driven but cursor-based program, commonly used here. Looked down upon for being not free.
  4. thunderbird from mozilla.com
    Both mutt and elm can be extensively customized, including choice of editor when composing messages, sorting of the displayed messages, etc. Your mail (to be read by any of the above programs) can also be pre-filtered to remove junk mail or to direct mail from certain people or on certain subjects into specific mailboxes or folders. See man filter or man procmail.)
  5. procmail e-mail filtering into separate folders and/or to remove spam. A sample .procmailrc file to put in your home directory can be found here


  1. vi the quintessential UNIX editor
  2. vim vi Improved
  3. emacs the 2nd (?) most popular UNIX editor - extremely extensible and customizable
  4. jed an emacs clone that includes syntax highlighting (modes for using colour for emphasis and automatic formatting of programs.
  5. jot the SGI mouse-based editor -- now superceded by:
  6. nedit much more powerful than jot
  7. pine a simple editor

Web browsing software

  1. Get Firefox!
  2. mozilla (mozilla or firefox)
  3. lynx (for character-based terminals - no graphics, and therefore fast)
  4. w3m also for character-based terminal, but better than lynx. It handles tables properly and can display images in-line if you wish.

Anti-virus/Adware/pop-up removal software

  1. Ad-Aware
  2. Spy-bot S & D (Search and Destroy)

Graphic design, image display and image manipulation software

    Graphic design and drawing

    1. showcase - SGI software - design and manipulation
    2. xfig - X-windows drawing program

    Image manipulation

    1. The Gimp a free clone of PhotoShop
    2. ImageMagick powerful command-line and menu-driven (see display image manipulation
    3. imgworks on SGI's only

Last revised: Tuesday, 17-Dec-2013 11:27:33 EST