On Jun 5, 2008, at 2:17 AM, Maurice Ho wrote:
How to color residues of a protein according to the electrostatic potential map generated by APBS? I could only color the molecular surface by loading the potential map. Please kindly advice. Thanks and regards, Maurice Ho
Hi Maurice, First, map the potential values to the atoms (assign them as attributes). Then you can color the atoms by those attribute values. After you have opened the protein structure and APBS map, start "Values at Atom Positions" (under Tools... Volume Data). In that tool: - Choose the protein as the "Molecule" and the APBS map as the "Volume data." If you didn't open the map yet, you can open it now using the Browse button. - Click the Histogram button to assign the atom values, which also automatically starts the "Render by Attribute" tool. The new attribute will be named based on the APBS map file name but with "value_" stuck on the front. There will be a histogram of values with vertical colored bars. These bars or thresholds can be moved around, added or deleted with Ctrl-click, and their colors changed to control the color mapping. You can click Apply to perform the coloring but keep the dialog up for further adjustments. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#colors It is also possible to color by attribute value with the command "rangecolor" instead of the graphical interface. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html I hope this helps, Elaine