Below are a few different images of each structure (shown at 1/3 size; use browser “save link as” to get files of images 1200px wide). These represent only a small sample of the possible variations in color and style, and even if none are quite what you need, they may help narrow your specifications.

• The structure you suggested for HIV1 protease (PDB 2HVP) does not have all atoms, only a backbone trace, so I used PDB 3PHV instead. Otherwise, I stuck with the suggested PDB entries.
  
  
• Without information on specific aspects of a protein you might want to highlight, I've just shown overall structures and in some cases, active site residues.
  
  
• In general, variations in color scheme, style, position, and background (including transparent background) would be simple to make, because I've saved the setup files for all of these.
  
  
• One thing that can't be done in Chimera is to draw curving dashed lines to represent missing parts (I see the caspases have lots of these); it only shows a straight line joining the “stumps.”

HIV-1 Protease (PDB 3PHV)

• see WebGL version of the first image below

Human Cytochrome P450 2C9 (PDB 1OG5, complex with warfarin)

• see WebGL version of the first image below

Human Caspase-7 (PDB 4FDL)

• orientations are the same as for procaspase-3 (I superimposed the structures beforehand); the left column is all one orientation, the right column another
• surfaces may be slightly misleading because parts of the structure are missing, as indicated by the dashed lines in the first lefthand image

below same as above except “flat” transparency

Human Procaspase-3 (PDB 4JQZ)

• orientations are the same as for caspase-7 (I superimposed the structures beforehand); the left column is all one orientation, the right column another
• surfaces may be slightly misleading because parts of the structure are missing, as indicated by the dashed lines in the first lefthand image

below same as above except “flat” transparency