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pyMol - Glossy surface

The glossy surface effect is probably the easiest and most efficient way to create proffessional looking images of your structure. However, many do not know how to do this, so here is a step by step guide.

1. Open pymol and load a PDB structure. My structure is called ast.pdb.

PyMol> load ast.pdb

Loading a structure in pyMol.

2. Display the surface (in this case for the entire structure).

PyMol> show surface

Displaying a surface.

3. Surfaces look (in my opinion) much better if we add a consistent color to it. I have chosen the color skyblue.

PyMol> color skyblue

Coloring the surface.

4. Ray trace the figure to give it some ligth just to check out how it looks before making the final adjustments (you can of course skip this).

PyMol> ray 400,400

Ray tracing the object.
Actually, the image is already quite nice, but it needs some adjustments to get the glossyness we want.

5. Adjust the specular reflection to the value of 250. You will not see any effect of this before you ray trace the image, so repeat step 4 to see the result.

PyMol> set spec_power, 250

Ray traced image with specular reflection power set to 250.
Now the surface is more plastic-like than before.

6. The final step is to adjust the specular reflection to a value of 2. This gives the glossy look that we are looking for. You will not see any effect of this before you ray trace the image, so repeat step 4 a final time.

PyMol> set spec_reflect, 2

Ray traced image with specular reflection of 2.
And that is all! By experimenting with different combinations of the specular power and reflection you can adjust how diffuse or sharp the reflection is going to be. You can easily create everything from shiny surfaces to more dull surfaces.
Final result.

Summary:

pyMol> load structure.pdb

pyMol> show surface

pyMol> color skyblue

pyMol> set spec_power, 250

pyMol> set spec_reflect, 2

pyMol> ray xxx,yyy

Depending on your preferences, choose a different color space than the defaul RGB. Personally I prefer the CMYK color space which forces PyMOL to restrict its use of the RGB color space to a subset that can be reliably converted to CMYK using common tools such as Adobe Photoshop.

pyMol> space cmyk

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