[Chimera-users] Solvent Accessibility

[Elaine Meng]

Hi Vinny,
Chimera does not calculate this directly, but there are a couple of  
ways to attack the problem.  It also depends on what exactly you mean  
by accessibility:  the square angstroms of solvent-accessible surface  
area for a residue, or that value normalized by the surface area in a  
model of the fully exposed state of that type of residue (often in an  
extended Gly-X-Gly peptide).

For the former, just the value of the solvent-exposed surface area of  
each residue, it is possible to do everything in Chimera without file  
editing, but there are several steps (also, I recommend Chimera  
version 1.2121 since there is a bug in step 4 in later versions,  
which we are now fixing):

(1) open the structure of interest
(2) delete all waters, ligands, etc. you don't want in the surface  
area calculation, for example using the command: delete solvent |  
ligand | ions
(3) open the Surface Area/Volume tool (Tools... Surface/Binding  
Analysis... Surface Area/Volume) use that to compute Accessible  
Surface (Gerstein) and show the resulting attribute in the Render/ 
Select by Attribute tool (these are the default settings). This  
generates the values for the ATOMS, which is shown as a histogram in  
the Render/Select by Attribute tool.  Alas, you still have to add up  
the values for the atoms to get totals for the residues, which is the  
next step:
(4) Choose Tools... Structure Analysis... Attribute Calculator and in  
that, Calculate attribute named whatever you want for RESIDUES (not  
atoms, which is the default setting) and enter the formula: sum 
(atom.accessibleSurface)
Also check the option to "Save calculation results to file."  This  
will write a text file listing the residue totals. The file will  
contain something like

attribute: whatever-name-you-specified
match mode: 1-to-1
recipient: residues
     #0:1.A    156.86
     #0:2.A    80.45
     #0:3.A    129.9
       ... etc. ...

The resulting residue attribute is also shown in the Render/Select by  
Attribute tool as a histogram.  (5) Here is the fun part:  you can  
move the sliders around on the histogram, add/subtract sliders, and  
change slider colors to control how the coloring is mapped to surface  
area values.  Click the Help button on the Render/Select by Attribute  
dialog to get more details if you wish.

For the latter, the normalized value, you'd have to get the values  
outside of Chimera.  In the past, I've used the GETAREA server for  
this purpose.  Here are the steps if you use GETAREA; some file  
editing is required:

(1) upload your structure to the GETAREA server, see
http://www.scsb.utmb.edu/getarea/area_man.html
click the "submission form" link to get the actual form
(2) edit the GETAREA results (pick whatever column of values is of  
interest; I used "Ratio (%)" which is the normalized value) into a  
text file with the format used by Chimera's Define Attribute tool.   
The Define Attribute format is described in:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ 
defineattrib.html#attrfile
(This is the same format written out in step (4) above.)  Most of the  
lines in the file are tab-separated columns where the first column  
specifies the residue and the second gives the value that should be  
assigned to that residue.
(3) choose Tools... Structure Analysis... Define Attribute and open  
the file you made
(4) use Render/Select by Attribute to color residues according to  
your new attribute (see (5) above for more info)

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 Oct 12, 2005, at 6:58 AM, Vincent Lynch wrote:

> To Whom It May Concern,
>
> I am new to Chimera (and molecular modeling in general) and cant
> figure out if I can color by residue accessibility to solvent and see
> the raw value of solvent accessibility.
>
> Thanks
> Vinny
>
>
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