ribbons-demo -n globin

Data Files:

The tetrameric human oxy-hemoglobin was taken from the Protein Data Bank (code is "1HHO"). The "1hho.pdb" file was edited to remove all but the main reference. The "1hho_*.pdb" files have undergone manipulation for a local research project. The crystallographically related dimer was generated, and renumbering done to conform to the peculiarities of XPLOR.

The *.coords file consists of only four filenames:
ls 1hho_A.pdb > globin.coords
ls 1hho_B.pdb >> globin.coords
ls 1hho_C.pdb >> globin.coords
ls 1hho_D.pdb >> globin.coords

A secondary structure assignment was made based on H-bonding:
pdb-pro-pdb 1hho_A.pdb 1hho_A.ss
pdb-pro-pdb 1hho_B.pdb 1hho_B.ss

The *.ribbons file consists of only four filenames (note the use of the same SS file, as the molecules are two-fold related):
ls 1hho_A.ss > globin.ribbons
ls 1hho_B.ss >> globin.ribbons
ls 1hho_A.ss >> globin.ribbons
ls 1hho_B.ss >> globin.ribbons

This file was then edited to add a special color file, "globin.color".

Separate files were generated for each of the four porphyrin rings and for each of the four iron atoms. This was done with the shell script "1hho_H.csh":
csh 1hho_H.csh

The *.model file was generated, and edited to give a different name and to reflect the tru center of the tetramer:
pdb-model 1hho_.pdb globin.model

The multimeric protein ribbon model is now ready for display.

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