ray creates a ray-traced image of the current frame. This command is used to make high-resolution photos fit for publication and formal movies. Please note, the ray command can take some time (up to several minutes, depending on image complexity and size).
For those who are making movies with PyMOL, Ray is one of the most commonly used last steps before stitching the frames together to compile the movie. Ray has many powerful features such as setting the size of the image -- and it still works even if the Viewport or screen is smaller than the requested output file dimensions.
ray [width,height [,renderer [,angle [,shift ]]]
angle and shift can be used to generate matched stereo pairs
cmd.ray(int width,int height,int renderer=-1,float shift=0)
Setting the Ray_trace_mode variable in PyMOL changes the way PyMOL's internal renderer represents proteins in the final output. New modes were recently added to give the user more options of molecular representation. New modes are: normal rendering, but with a black outline (nice for presentations); black and white only; quantized color with black outline (also, very nice for presentations; more of a cartoony appearance).
# normal color set ray_trace_mode, 0 # normal color + black outline set ray_trace_mode, 1 # black outline only set ray_trace_mode, 2 # quantized color + black outline set ray_trace_mode, 3 set ray_trace_mode, 1 # (or 2 or 3; best with "bg_color white;set antialias,2") # These two new modes -- 2 and 3 -- are cool cartoon looking modes.
Here are the example images for the new modes
Perspective Example Images
PyMol 0.97 and prior used orthoscopic rendering -- that is, no perspective. Upon the arrival of 0.98 and later, we get perspective based rendering at a cost of a 4x decrease in render speed. If you want perspective
set orthoscopic, off
set orthoscopic, on
To magnify the effect of perspective on the scene,
set field_of_view, X
where 50<X<70. Default is 20. 50-70 gives a very strong perspective effect. Nb. the field of view is in Y, not X as one would expect.
renderer = -1 is default (use value in ray_default_renderer)
renderer = 0 uses PyMOL's internal renderer
renderer = 1 uses PovRay's renderer. This is Unix-only and you must have "x-povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and "tmp_pymol.png".
# ray trace the current scene using the default size of the viewport ray
Specify Image Size
# ray trace the current scene, but scaled to 1024x768 pixels ray 1024,768
# ray trace with an external renderer. ray renderer=0
High Quality B&W Rendering
# Black and White Script load /tmp/3fib.pdb; show cartoon; set ray_trace_mode, 2; # black and white cartoon bg_color white; set antialias, 2; ray 600,600 png /tmp/1l9l.png
High Quality Color
# Color Script load /tmp/thy_model/1l9l.pdb; hide lines; show cartoon; set ray_trace_mode, 3; # color bg_color white; set antialias, 2; remove resn HOH remove resn HET ray 600,600 png /tmp/1l9l.png
Ray Tracing Stereo Images
"help faster" for optimization tips with the builtin renderer. "help povray" for how to use PovRay instead of PyMOL's built-in ray-tracing engine. For high-quality photos, please also see the Antialias command. Ray shadows for controlling shadows.
See also Ray Tracing.
How do I ray trace a publication-ready (~300dpi) image using PyMol?
This answer is in the Advanced Issues (Image Manipulation Section).