zone tool in volume rendering
I've been using the new mask tool to extract features along surfaces, which is useful in its own right for generating separate maps of segmented areas. but, if I wish to color a region around a surface (or between surfaces) without generating a new map, I am not sure how to do this - the 'zone' and 'color zone' tools in Volume viewer expect atoms or marker files. I had thought about loading multiple files of these surface regions after segmenting them out, each with their own color, but loading them together produces the ordering problem with the volume rendering. also, loading multiple volumes consumes a lot of memory and I run short of memory. is there currently a way to color arbitrary regions in a volume rendering? for example, rendering all data within 60 A of a surface with a different color than the rest of the volume, or coloring a region between two surfaces a different color, analogous to the 'sandwich' option of the mask tool. thanks, -Jeff
Hi Jeff, The capability you need is to make a mask (integer array) that records which region each grid point belongs to. Then you would be able to choose colors for each numbered region. You could define the regions using the "mask" command which can currently only make a new map. This support for masks does not exist yet in Chimera. I intend to add support for masks this year. So the current ways of coloring surfaces are: color zone dialog (color points near markers), surface color dialog (color according to values in a second map, or gradients of a map, or by radius, or height above a plane), or single color. Those methods are for surface/mesh coloring. For solid style volume rendering it is only possible to color according to the grid point values. These coloring methods are limited by the user interface. The underlying rendering code can color a surface or solid in any way you like, though defining other colorings requires writing Python code. Tom
participants (2)
-
Thomas Goddard -
William Jeffrey Triffo