Hi Huy, If I understand correctly, you want (1) a isosurface of the density map (2) colored by the gradient in that same map. (1) If you open the density map in Chimera, it will automatically start Volume Viewer, in which you can adjust the isosurface display (contour level(s), smoothing, etc.). More details on Volume Viewer: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html (2) Then you can use Surface Color (listed under Tools... Volume Data in the main menu, or in the Volume Viewer Tools menu) to color that isosurface by the data gradient. You do not have to make a separate map with the gradient. In Surface Color, choose the option to use the "gradient norm" of the density map you already opened. Then you can adjust how colors should map to the gradient norm values. More details on Surface Color: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/surfcolor/ surfcolor.html I hope this is what you had in mind. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote:
Hi, I'm pretty newbie for Chimera. Anyone knows there is a function to display a density map as a gradient map?
My purpose is: - Having one density map displayed as a surface rendering map - Having another different density map displayed as a gradient map only on the surface of the surface rendering map above.
Thanks a lot, Huy