ribbons-demo -n ubiq

Data Files:

The small protein ubiquitin solved in this laboratory was taken from the Protein Data Bank (code is `1UBQ'). The file was edited to remove all but the main reference and protein atoms and named `ubiq.pdb'.

A secondary structure assignment was made based on H-bonding:
pdb-pro-pdb ubiq.pdb ubiq.ss

This file was then edited to replace the 'S' at the ends of the sheets with an 'A' to produce `arrows' on the sheet. The first residue was also changed, from `coil' to "sheet" ( program doesn't know how to calculate N-terminal hydrogens ).

The *.ribbons file consists of only one filename:
ls ubiq.ss > ubiq.ribbons

This file was then edited to add a special color file, `protein.color'.

The *.coords file consists of only one filename:
ls ubiq.pdb > ubiq.coords

The *.model file was generated:
pdb-model ubiq.pdb ubiq.model

The protein ribbon model is now ready for display.

Image File: $RIBBONS_HOME/rgb/ubiq.rgb

The file ubiq.ss was edited to add arrows to the ss key. The model was displayed with default settings on the Ribbon Panel for everything except:
Sequence Color = `seq'
Sheet Style = `Square'
Helix Style = `Flat'
Coil Style = `Circle'
Helix Texture = `Sided'

The light source was moved overhead with the Color Panel. The image was saved from the Geom Panel. Labels were added with the ilabel command:
ilabel ubiq0.rgb ubiq.rgb

Ribbons User Manual / UAB-CMC / carson@cmc.uab.edu