
Hey Folks, I'm using Chimera to create a surface colored representation of a virus based on radius. That was not the hard part, my question is how do you make a key to show the scale of coloring. I cannot find that in the documentation, faq nor the server list. If it's there and I missed it sorry but you point it out to me and if it's not an option any suggestions on how to create one. Thanks. Alex

Hi Alex, Chimera is not able to produce a color key for coloring done with the Surface Color tool. I think the best way to proceed is to use Photoshop or GIMP (free). I believe you can make rectangles with linear color gradients in both those image editting programs. You would need to record the radii and (red, green, blue) color values for each radius used in Chimera and use the same colors in Photoshop or GIMP. The trouble with making the key in Chimera is that Chimera has very limited 2-D graphics capabilities -- only 2D text labels are available. I haven't tried making the color key in Photoshop or GIMP and it may prove difficult. Here is a way to make the color bar in Chimera that makes a cube and colors it with the Surface Color tool by distance along the X axis. Then you save the image, cut a strip of it out using Photoshop and add labels. Use menu entry Tools / Utilities / Benchmark, set the standard model size to 256 in the Benchmark dialog and press the "surface" button under the "Show standard model" line (*not* the surface button on the top line). This shows a cube with extent -1 and +1 along each axis. The surface is composed of triangles on a 256 by 256 grid on each square face. The surface will be listed in the menu in Surface Color dialog that you used to do the radial coloring -- it will just show its model number since it has no name. Choose that surface in the Surface Color dialog and switch to coloring it using "Height". Set the axis to "1 0 0" (x-axis). Hopefully you still have the radial colormap shown in the Surface Color dialog. Now adjust the data values by dividing them by 100 or some other value so that they lie in 0 to 1. Maybe you will want to subtract a constant so that the values range from about -1 to 1 so most of the cube is colored. Press the Color button to show this coloring. Press the orient button on the volume dialog to show the standard orientation (box aligned with xy axes). Save the Chimera image. When you add text labels in Photoshop to a strip cut from this image just linearly interpolate along the strip between the smallest and largest radius -- that is exactly correct. Looks like I could add to Surface Color some code to make the color key using a rectangular Chimera surface without all the rigamarole. I've added that to my requested feature list although I do not expect it to be implemented soon because there are many higher priority features to add. Tom
participants (2)
-
Alexander Rusnak
-
Thomas Goddard