Create a PDB file with your coordinates in it (e.g., pep.pdb)
Type:
setup ribbons_265
pdb-model pep.pdb pep.model (make model)
pdb-atom-sph pep.pdb pep.sph (make spheres for atoms)
pdb-bond pep.pdb pep.cyl (make cylinders for bonds)
ls pep.sph > pep.atoms (create list file for atoms)
ls pep.cyl > pep.bonds (create list file for bonds)
ls pep.cyl > pep.texts (create list file for labels)
ribbons
Orient your molecule and find an atom close to where you want a label, note the atom ID.
From the pep.sph file, copy the line describing the above identified atom to a new file called, label1.sph.
Edit label1.sph and change the last column to your label instead of the atom ID.
Type: ls label1.sph >> pep.texts
Click in the Ribbons window File | Re-read Data | *.texts
Click in the Ribbons window Edit | Text Control Panel and under Text Lists activate pep.sph and turn off the atom labels.
Click in the Ribbons window Edit | Text Control Panel and under Text Lists activate label1.sph
Now you can shift the label around or change the Font and Overall Color (If you can't move the label enough, edit the coordinates in the label1.sph file to re-define the starting place.)
You may make additional labelx.sph files, just list them in pep.texts.
Click the Overall Color button to make the label 13~Black
Click in the Ribbons window View | B/W Background
Click in the Ribbons window Edit | Atom Control Panel | Overall Color | Gray | Radius Scale | 0.25 | Complexity | 1.00
Click in the Ribbons window Edit | Bond Control Panel | Overall Color | Gray | Radius Scale | 1.00 | Complexity | 1.00
Click in the Ribbons window View | Outline Image | Linewidth = 2
Click in the Ribbons window Edit | Light Control Panel | Depthcue Fog On | Fog Density 0.15
Click in the Ribbons window View | Stereo | Side-by-side