Uppsala Software Factory - Tutorials

Here I will add tutorials every now and then explaining how to do things that require the use of more than one program. They will not go into the details of separate programs; for that you will still need to consult the appropriate manual(s).
  1. Dimensions and volumes, and how to "guestimate" them using USF programs.

  2. Recognising your fold, using DEJAVU, LSQMAN, DEJANA, and O.

  3. Recognising a motif from your protein in other protein structures, using SPASM, SAVANT, DEJANA, and O.

  4. Local density correlation used to assess or validate differences between related protein crystal structures.

  5. Introduction to Structural Databases. Tutorial prepared for the 1999 EMBO Practical Course in Bioinformatics in Uppsala. This is an adaptation of a tutorial created by Tom Taylor. It was updated in August, 2001.

  6. Visualisation of planes. This explains how to visualise least-squares planes in O. The tutorial uses only Uppsala programs (MOLEMAN2 and O). In the example, a chain of nine twisting glucoses inside CBH I is visualised.

  7. Visualisation of tunnels. This explains how to visualise tunnels and other cavities in your protein that are connected to the outside world. The tutorial uses only Uppsala programs (MOLEMAN2, VOIDOO, MAMA, MAPMAN, and O).

  8. Biomolecular morphing. This explains how to visualise transitions between conformational states etc. in a jiffy, using LSQMAN and a molecular graphics program (e.g., O). The results can be published on the web, e.g. as animated GIF files.

  9. SBIN. This explains how to use the programs in the SBIN package to generate sequence patterns and profiles based on superimposed protein structures, and how to scan these against sequence databases such as SWISS-PROT.

See also the Teaching & education page.

USF Latest update at 15 July, 2002.