A secondary structure assignment was made based on H-bonding:
pdb-pro-pdb calmod.pdb calmod.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. ( at Babu's advice, set 26-28, 62-64, 99-101, 135-137 to sheets, and lengthened helices 4 and 6 by one residue, helix 8 by 2. )
The *.ribbons file consists of only one filename:
ls calmod.ss > calmod.ribbons
This file was then edited to add a special color file, `protein.color'.
The *.coords file consists of only one filename:
ls calmod.pdb > calmod.coords
The calcium atoms were separated placed in a separate file:
GREP HETATM calmod.pdb > calmod_cal.pdb
The calciums were turned into silver spheres (color-11)
pdb-range-sph calmod_cal.pdb calmod_cal.sph
( input line-1 at terminal: 1 4 11 )
( input line-2 at terminal: ctrl-D )
The *.atoms file consists of only one filename:
ls calmod_cal.sph > calmod.atoms
The cylinders to model the helix were created in several steps.
First, a list was prepared of the residue ranges in the helices:
ss-hx-range calmod.ss calmod_hx.run
Next the alpha carbons in these ranges are fit to ideal helices:
pdb-hx-fit calmod.pdb calmod_hx.run > calmod_hx.fit
Finally the fit output is converted to bond format:
hx-dipole-cyl calmod_hx.fit calmod_hx.cyl
The *.bonds file consists of only one filename:
ls calmod_hx.cyl > calmod.bonds
The *.ss file was enhanced to include coloring by equivalent helices in the domains and by mainchain dihedral values.
The file calmod_hx.run was edited to chose colors for the ranges,
then a new *.ss file was created (the old thrown replaced):
pdb-range-ss calmod.ss new.ss
mv new.ss calmod.ss
Next `rama' and `omega' keys were added:
pdb-rama-ss calmod.pdb calmod.ss
The *.model file was generated:
pdb-model calmod.pdb calmod.model
The protein ribbon model, plus atoms, plus `bonds' is now ready for display.
The color #11 (silver) was modified with the Color Panel to
add Blue Emission, to produce the glowing calcium atoms.
The Geom Panel had the default settings except:
Sphere Radii = `1.25'
Bond Radii = `1.35'
Cylinder Depth = `24'
The image was then saved.