[Chimera-users] Tips for making density map images.

Thomas Goddard goddard at cgl.ucsf.edu
Mon May 21 11:40:38 PDT 2007

   Here are some suggestions for making density map images in Chimera 

   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.


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