On Feb 22, 2009, at 4:48 PM, Harinathachari Bahudhanapati wrote:
Dear Elaine, Chimera is getting more exciting to work with than ever. I think you guys are the best in the field. About per-model clipping...
When I tried, I was not able to find how to color the clipped plane based on atom B-factors? I was able to give a color (single color) only but not based on atom B-factors or other attributes like SAS, SES, electropotential. I am not sure if modeled PDB files still have B-factor details. I saw an image on the chimera website on the feature highlights (B-factor coloring) and I wondered if I can get few more details on this feature. I am trying to make a few pictures for my paper. Thank you elaine, sincerely, Hari
Dear Hari, Thanks for your kind words! Yes, there is a trick to coloring planar surface caps by B-factor or some other attribute, as in that figure: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> First, color the atoms by the attribute (Tools... Depiction... Render by Attribute), which would also color the actual molecular surface but not the planar cap where it is clipped. Then, select the atoms and use Color Zone (also under Tools... Depiction) to color the planar cap to match the nearby atoms. Render by Attribute: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render> Color Zone: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/ colorzone.html> I've been wanting to write a tutorial on how to make that figure, but haven't had the time! I also increased the "mesh subdivision factor" in the Surface Capping dialog to 3. Coloring by electrostatic potential is different than coloring by an atom attribute. To color the planar cap by electrostatic potential, you would use Electrostatic Surface Coloring, but it requires a potential map previously created with some other program such as DelPhi. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html