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ray creates a ray-traced image of the current frame.

Varying settings to play with rendering options

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  • 1Details
    • 1.3Settings
      • 1.3.2Perspective
        • 1.3.2.1Perspective Example Images
    • 1.4Performance
    • 1.5Examples

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.

Image, not ray traced.
Image, ray traced.

Usage

angle and shift can be used to generate matched stereo pairs

width and height can be set to any non-negative integer. If both are set to zero than the current window size is used and is equivalent to just using ray with no arguments. If one is set to zero (or missing) while the other is a positive integer, then the argument set to zero (or missing) will be scaled to preserve the current aspect ratio.

PyMol API

Settings

Modes

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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).

Note: Mode 3, the quantized color one, sort of burns the background if you're using this setting. This will make a pure white background somewhat 'offwhite'; thus, a poster would look poor because you could see the border for the image. If you'll be using this mode, try the ray_opaque_background setting.

Here are the example images for the new modes

  • set ray_trace_mode,1

  • set ray_trace_mode,2

  • set ray_trace_mode,3

Perspective

Perspective Example Images

  • Example with Perspective Turned Off

  • Example with Perspective Turned On

  • Example with Perspective Turned On and Field of View Set High (70).

Notes

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

Otherwise

To magnify the effect of perspective on the scene,

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

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 'povray' in your path. It utilizes two temporary files: 'tmp_pymol.pov' and 'tmp_pymol.png'. Also works on Mac via Povray37UnofficialMacCmd but it needs to be in your path as 'povray'.

Performance

  • The ray performance depends on distance between camera and molecule.

If the distance is big rendering takes much time. If the distance is too small distant parts of molecule dissolve.

  • Too close to molecule

  • Normal distance

  • Tip: If you have a rather complicated scene that is zoomed into only a part of the molecule, you can speed up the ray tracing by hiding everything else outside of a certain range of the zoomed-on point. For example, if I have a large molecule and I'm looking only at the 30-atom ligand bound to it, then I can do something like the following:

As an example of the efficacy of this method, I ray traced a rather complex scene with all the atoms visible here's the output of ray:

Download Outline For Mac 1.3.1Download Outline For Mac 1.3.1

and here is the result when I soft-clipped everything else using the above method:

The two images in the following gallery show the results of the rendering.

  • normal ray tracing. This took twice as long to make as the image to the right. Same size, and DPI.

  • manually hiding things you won't see anyway. This took 1/2 the time to render as compared to the same sized & DPId image at left.

Memory

If memory is an issue for you in PyMOL, try executing your rendering from a script rather than a PyMOL session file. An unfortunate unavoidable consequence of the fact that we use Python's portable, platform-independent 'pickle' machinery for PyMOL session files. Packing or unpacking a Session or Scene file thus requires that there be two simultanous copies of the information to reside in RAM simultaneously: one native and a second in Python itself.

So when memory is a limiting factor, scripts are recommended over sessions.

Examples

Simple

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Specify Image Size

Specify Renderer

High Quality B&W Rendering

Black and White (ray_trace_mode,2); click to see full image

High Quality Color

Color mode (ray_trace_mode,3); click to see full image

Ray Tracing Stereo Images

See Stereo_Ray

See also

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  1. '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.
  2. See also Ray Tracing.
  3. Desaturation Tutorial -- A good resource for making nice B&W images from color images (desaturation).

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User comments

How do I ray trace a publication-ready (~300dpi) image using PyMol?
This answer is in the Advanced Issues (Image Manipulation Section).
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