feat: enhance 3D structure visualization with consistent coloring and opacity

[t03i]

Summary

• Add secondary structure coloring to PyMOL and ChimeraX family scripts
• Add optional --opacity parameter for transparency control
• Maintain backward compatibility with existing benchmark calls

Changes

• Red helices, blue strands, gray coils/loops coloring
• Optional --opacity parameter (0.0-1.0, default 1.0)
• Consistent coloring between 2D diagrams and 3D structures

Test plan

• Verify backward compatibility
• Test opacity values 0.3, 0.5, 0.7, 1.0
• Test with cobra and KLK family structures