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).
and volumes, and how to "guestimate" them using USF programs.
your fold, using DEJAVU, LSQMAN, DEJANA, and O.
a motif from your protein in other protein structures, using
SPASM, SAVANT, DEJANA, and O.
density correlation used to
assess or validate differences between related protein
- 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.
- 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.
- 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).
- 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.
- 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.
Latest update at 15 July, 2002.