VMD User's Guide

Name Description Default Render CommandTachyon 1 Very fast, high quality tachyon -aasamples 2 -mediumshade %s -formatmultiprocessor ray tracer TARGA -o %s.tgaPOV3 2 POV-Ray 3.x ray tracer povray +H500 +W400 -I%s -O%s.tga +D +X +A+FTRayshade 3 Rayshade ray tracer rayshade < %s > %s.rleRadiance 4 Radiosity ray tracer oconv %s > %s.oct; rview -pe 100 -vp -3.5 00 -vd 1 0 0 %s.octART 5 Simple VORT ray tracer art %s 500 6501 See http://www.photonlimited.com/ for more info.2 See http://www.povray.org/ for more info.3 See http://www-graphics.stanford.edu/ cek/rayshade/rayshade.html for more info.4 See http://radsite.lbl.gov/radiance/HOME.html for Radiance5 Available from ftp://gondwana.ecr.mu.oz.au/pub along with the rest of VORT packageTable 7.2: Supported ray tracing formats.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 drawnusing a number of polygonal facets, curved surfaces may be rendered entirely smoothly in thefinal 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 usedfor performing complex shading. VMD’s real-time rendering of these material propertiesis often simplistic or limited compared to full-fledged photorealistic renderers, so there canpotentially 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 zoomingthe camera so that the image size is acceptable again. This will significantly decrease theperspective effect, but is not a true orthographic projection.• The rendering commands do not currently support stereo output, so even if the display iscurrently in stereo mode, a non-stereo perspective will be used for the rendering programinput script; Rendering in stereo is accomplished by setting the display mode to “left”, thenrendering an image, followed by “right”, and rendering again. This will yield a stereo pair tothe 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 labeltext will not appear, although the lines of bond, angle, etc. labels will be drawn. The onlyexception is in Postscript output, which supports text output.86