Ubiquitin ribbon drawing.

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:

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-CBSE / carson@uab.edu