[Chimera-users] coloring plane by ESP

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 29 09:10:33 PDT 2013

Hi Marek,
Just thought I'd mention that in Chimera you can color a plane that is in any orientation by the values in an ESP map.

Unfortunately it doesn't work with the planes from Axes/Planes/Centroids, but you can create a rectangular plane with specified height and width with command "shape rectangle".  Then you can open the molecule and the ESP map, activate/deactivate models (freeze/unfreeze them) and use the mouse to position the rectangle however you like in relationship to the molecule.  Then you can use the "Surface Color" tool (aka Electrostatic Surface Coloring) to color the rectangle by the ESP map values.

If you didn't already have an ESP map, you could use the PQR and APBS tools in Chimera to calculate one with APBS, or use the Coulombic Surface Coloring tool with option to "Compute grid" (i.e. make ESP map).

Attached image is for 3eeb chain B, ESP map file 3eebB.phi ( available from link near bottom of the Surface Properties image tutorial <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> ), and rectangle created with command:

shape rectangle height 50 width 50 widthdiv 100 heightdiv 100 center protein

It shows the area of strong positive potential near where the highly negatively charged ligand binds.

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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