[Chimera-users] creating volume maps

[Elaine Meng]

Hi Nils,
You could do that, but there are several caveats, which I will  
describe below.  First, some alternative suggestions:

(a) why not just use the solvent-accessible surface area of each  
atom?  Perhaps the reactive species is bigger than water, but you can  
just increase the probe radius as needed to to approximate this  
species.  As soon as you calculate a molecular surface, the per-atom  
and per-residue solvent-accessible and solvent-excluded areas are  
assigned and can be saved or used in various ways.  Details:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003813.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
 >

(b) however, it sounds like your proposed measure involves not only  
the accessible surface area of an atom, but the convexity of the  
molecular surface at that atom.  If that is true, you could use this  
measure of convexity:  solvent-accessible surface area divided by  
solvent-excluded surface area (solvent-accessible is where the probe  
center goes, solvent-excluded is where the probe surface goes).   
Exactly this quantity is calculated in the Attributes tutorial, part  
2, and shown in the figure with color:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2 
 >

As to what you described, here is an example of how to do it (commands):

open 1zik
molmap :17.a at oh 5 modelId 1
surf
mask #1 #0
measure volume #1
measure volume #2

which reports in the Reply Log 114 A*3 for the original volume, 53 A*  
for the masked volume.

See the manual pages for molmap, mask, and measure (requires Chimera  
1.4):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

The caveats:
- Chimera does not show the solvent-accessible surface but the solvent- 
excluded, so you would be masking using the latter
- not sure what you would use for the Gaussian resolution in the  
molmap command
- you might want to make the surface of the Gaussian sphere blob more  
finely triangulated for these measurements, which could be done with  
the Volume Viewer GUI or the volume command (see surface and mesh  
options)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 29, 2009, at 4:40 AM, Nils Becker wrote:

> Hi,
> I would like to use chimera for measuring the steric accessibility of
> particular atoms in a structure to reactive species in solution. To do
> that I had the following idea:
>
> 1. create a volume map which represents a solid sphere centered on the
> atom in question (alternatively, a Gaussian blob), with some chosen  
> radius.
>
> 2. mask this sphere using the solvent accessible surface of the  
> protein
> (for example, if the atom is at the surface and the surface is flat,
> half of the sphere would be cut away)
>
> 3. measure the volume of the remaining piece of the sphere.
>
> So now my question is: can this work, and how can I generate the  
> sphere
> in step 1. ?
>
> thanks for any advice!
> Nils