[Chimera-users] Fwd: accessible surface area for electron density maps

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 27 13:04:25 PDT 2009

Hi everybody,
What Miguel describes is how to make the displayed molecular surface  
look more like a solvent-accessible surface by moving it 1.4 A  
outward, even though it is really calculated as a solvent-excluded  

However, it is not necessary to do that if you are interested in the  
area values rather than the display: areas are reported and assigned  
as attributes for both types of surface even though only the solvent- 
excluded one is shown.

In fact, if you will be using the area values, you should NOT perform  
those adjustments, because the area of that displayed surface (which  
is now expanded from the solvent-excluded surface but is still not  
exactly the solvent-accessible surface) will be reported as the  
solvent-excluded area, and even bigger values reported as the solvent- 
accessible areas.

Also in agreement with what Miguel said, the surface calculation does  
not use density, it only uses atomic positions and radii.

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

On Mar 27, 2009, at 10:35 AM, Miguel Ortiz Lombardia wrote:

> Hi,
> My understanding is that the solvent accessible surface is not  
> (yet) available in Chimera. However, Elaine showed me once how to  
> get more or less such a surface:
> 1. Before calculating the surface issue the chimera command:
> 	vdwdefine +1.4
> which adds 1.4 A (roughly the usual radius for the water probe) to  
> all atom radii
> 2. Show the surface
> 3. On the Model Panel, select the surface and under "attributes"  
> change the probe radius to 0.5 It should be 0.0 but this is not  
> possible. This means that intersections of atom spheres will be  
> smoothed slightly. Still, the surface represents almost correctly  
> the solvent accessible one.
> The error on this surfaces doesn't depend directly on the quality  
> of the electron density but on the accuracy of the atoms positions.  
> Which of course depends on the data...
> I hope it helps,
> Miguel

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