[Chimera-users] coloring residues according to electrostatic force

[Elaine Meng]

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