Here are some suggestions for making density map images in Chimera 1.2382. White background color. Set with two menu entries Actions/Color/Background and Actions/Color/White. To make white the default use Favorites/Preferences, category Background, set background color button to white and press Preferences dialog Save button. Surface smoothing. Use volume dialog Features/Surface-And-Mesh-Options and click "Surface smoothing..." checkbutton. To make this the default, turn it on then use Features/Save-default-dialog-settings. Close the surface-and-mesh-options panel before saving the settings or it will always be shown taking up alot of space. Image supersampling. Removes saw-tooth edges from saved images that are especially visible with white background. Does this by making a larger image in memory then averaging down to a smaller size. When saving an image you see many small pieces flash by in main window if supersampling is being used. To turn it on use File/Save-image, press the Image Setup button in the save image dialog, then set Supersample to 3x3 in the preferences dialog that appears. Press the Save button in the preferences dialog to make this the default. For Chimera versions after 1.2392 this will look different. Supersample will be an option on the save image dialog. Saving image same size as on screen. To make a saved image the same size in pixels as it appears in the Chimera window press the Get Pixels button in the File/Save-image dialog. In Chimera versions after 1.2392 this will be the default. Silhouette edges. To add black edges around maps that makes it easier to see when part of map is in front of another part use Favorites/Side-view, choose the Effects tab in the viewing dialog that appears, click on silhouette edges. Save raytraced image. Gives glossy appearance and shadows. Use File/Save-image and set "Raytrace with POV-Ray" to True. Make back parts of surface darker. Use Favorites/Side-view and move the right vertical yellow line towards the left. The surface gets dimmer from half way between the yellow lines to the right yellow line. Your eye position in this side view is shown as the square at the left and the red lines indicate how wide your field of view is. If you move the right yellow line (rear clipping plane) it will hide parts of the map -- everything to its right is invisible. Probably want to avoid that. Make recesses in surfaces darker to improve sense of depth. Use Tools/Volume-data/Surface-color. For spherical virus color the surface using "Radius", use 2 colors, Gray pattern, press "Set full range colormap values" to get minimum and maximum surface radius, press Color. You may need to press the Center button if the virus map is not centered at (0,0,0), and also press the "Set full range..." button again in that case. Probably you'll want to modify the minimum and maximum radius to get the best effect, also maybe adjust the two colors. For filaments use "Cylinder radius". Make recesses darker for asymmetric maps. This is a bit trickier than for spherical or cylindrical maps. For ribosomes or other asymmetric maps first create a blurred version of the map using Tools/Volume-data/Gaussian-filter. This tool has to be downloaded separately from the Chimera experimental features web page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html and installed. Choose a gaussian width of about 1/3 the diameter of the surface (in angstroms, maybe 30 for a ribosome) and press Filter. Use the Tools/Volume-data/Surface-color and color the original map using the gaussian smoothed map. High values of the Gaussian smoothed map are in the interior and should be made a dark color. This makes the perception of depth dramatically better. Tom
