Caveats

When VMD creates the output file it will try to match the current view and screen size. For the most part it does a good a job but there can be some problems. The colors in the final raster image can sometimes look different from what is seen in the VMD graphics window. This is because the external rendering programs use different shading equations and algorithms from what VMD uses.
Potential rendering discrepencies include:

• Geometry may look slightly different; in VMD curved surfaces are polygonalized and drawn using a number of polygonal facets, curved surfaces may be rendered entirely smoothly in the final output (which is generally looked upon as an improvement!)
• The rendered object colors or intensities may be slightly different due to different colormaps, gamma values, or lighting models; This is particularly true with the material properties used for performing complex shading. VMD's real-time rendering of these material properties is often simplistic or limited compared to full-fledged photorealistic renderers, so there can potentially be big differences between implementations of transparency, specular highlights, etc.
• Many of the external renderers do not support true orthographic rendering. This can be ``faked'' by translating the camera very far away from the molecule, followed by zooming the camera so that the image size is acceptable again. This will significantly decrease the perspective effect, but is not a true orthographic projection.
• The rendering commands do not currently support stereo output, so even if the display is currently in stereo mode, a non-stereo perspective will be used for the rendering program input script; Rendering in stereo is accomplished by setting the display mode to ``left'', then rendering an image, followed by ``right'', and rendering again. This will yield a stereo pair to the best of VMD's ability with the external rendering program.
• The near and far clipping planes are ignored by all external renderers;
• Text is generally not available as a graphics primitive in the renderer scene languages, so label text will not appear, although the lines of bond, angle, etc. labels will be drawn. The only exception is in Postscript output, which supports text output.
• Dotted spheres are not drawn with dots.
• The background color may be black, as not all output formats support a background color other than black;