Software

Below you find a short list of software that may prove useful when working with protein structures. Yasara is required if you want to do the 3D drug design or the Retinitis pigmentosa practicum. The rest of the software is optional.
You may need a password to be allowed to install the software on your system. In such cases, ask your system administrator for more information.

• Yasara is an important tool if you want to study proteins in 3D. It is easy to install:
  • Download and install Yasara view, using the instructions from the Yasara website.
  • Then download and unpack the Bioinformatics@school course files.
  • You now have three folders/directories: pdb, sce, and mov. Move or copy the contents of each folder to the corresponding folders in Yasara's installation directory.
  • You are now all set to go.
  Additional information about using Yasara can be found in the More in 3D section.
  
  
• MRS is used a lot in bioinformatics. Sometimes even so much that the MRS server gets swamped. In such cases you can use one of these alternative MRS servers:
  • MRS @ EMBnet
  • MRS @ UNAM
  Note: These MRS servers look a bit different and may give slightly different results.
  
  
• Python is a so-called scripting language. It is used to automate certain tasks and to do simple calculations. We supply Python because it enables a few extra options in Yasara, but there is other fun stuff you can do with it.
  Python is already installed on most Linux systems. Here, you can download installation packages for Windows and OS X. The Python download page has more information about installing Python (also for Linux).
  
  
• The Persistence of Vision Raytracer is a tool to make nice pictures of 3D computer objects. Such programs are commonly used in the movie industry (think: Shrek and Finding Nemo). We use it to make pictures of proteins in Yasara (more here). There are even professionals who make nice pictures of molecules for a living.
  Here, you find installers for Windows, Linux and OS X. Visit the POV-Ray download page for more information about installing.
  
  
• The PowerPoint viewer 2007 enables you to view PowerPoint presentations without needing to buy the whole program. Unfortunately, there is only a Windows version.