[Chimera-users] buriedArea calculation: MSMS vs Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 1 11:26:04 PDT 2016


Hi Bala,
It is giving you all the details in the Reply Log, as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>

A surface is calculated for each set of atoms separately (surfA, surfB) and for their combination (surfAB). 

How much is buried for A?  it is the area of surfA minus the area of A-atoms-only in surfAB
This is generally not exactly the same as the buried area of B, which is the area of surfB minus the area of B-atoms-only in surfAB.  The sum of the buried areas of A and B is (surfAB - surfA - surfB), as you said.  However, this is about twice the interface area because you are counting what is buried on both sides even though they form one interface. The average is simply half of (surfAB - surfA - surfB). 

So you could use the average or twice the average, depending on what definition of the buried area you prefer.

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



On Apr 1, 2016, at 11:11 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:

> Friends,
> I have a task to calculate how much is the buried SASA during formation of a bi-domain protein. The usual relation to obtain is (SAS-domain1 + SAS-domain2) - SAS-complete
> 
> I have a difficulty to understand how the calculation is performed in Chimera. As a test case, i used the 1crn.pdb and performed using MSMS and in Chimera.
> 
> MSMS calculation (Input: msms -if 1crn.xyzr -probe_radius 1.5 -density 3.0)
> Complete system SAS = 3054.258 , (residue 1-23) pA = 2143.122 , (residue 24-46) pB = 2324.809,  hence total buried =  ( pA + pB) - 3054.258 = 1413.673
> 
> Chimer calculation
> surf #0  (Reply log: SAS = 3022.61)
> 
> measure buriedArea :1-23 :24-46 probeRadius 1.5 vertexDensity 3.0
> Status line : SAS = 697.876, SES = 423.938
> 
> Reply log: Buried solvent accessible surface area
> B1SAS = 681.191, B2SAS = 714.56, BaveSAS = 697.876
> (A1 = 2116.11, A2 = 2302.43, A12 = 3022.79 = 1434.92 + 1587.86)
> 
> I am not getting the calculation (and the motive as well) of the  BaveSAS in the following part of the code. 
> 
> q1) What is Chimera actually doing here 
> q2) Which one i should report, raw buried SAS or BaveSAS in your opinion ?
> 
> ----------------------------------
> for ai,a in enumerate(atoms1):
>     a.buriedSESArea = aareas1[ai,0] - aareas12[ai,0]
>     a.buriedSASArea = aareas1[ai,1] - aareas12[ai,1]
>     ases121 += aareas12[ai,0]
>     asas121 += aareas12[ai,1]
> for ai,a in enumerate(atoms2):
>     a.buriedSESArea = aareas2[ai,0] - aareas12[n1+ai,0]
>     a.buriedSASArea = aareas2[ai,1] - aareas12[n1+ai,1]
>     ases122 += aareas12[n1+ai,0]
>     asas122 += aareas12[n1+ai,1]
> careas1, careas2, careas12 = s1[4], s2[4], s12[4]
> ases1, asas1 = area_sums(careas1)
> ases2, asas2 = area_sums(careas2)
> ases12, asas12 = area_sums(careas12)
> bsas1 = asas1 - asas121
> bsas2 = asas2 - asas122
> bsas = 0.5 * (bsas1 + bsas2)
> bses1 = ases1 - ases121
> bses2 = ases2 - ases122
> bses = 0.5 * (bses1 + bses2)
> 
> Thanks,
> Bala
> 
> 
> 
> 
> -- 
> C. Balasubramanian
> 
> 
> 
> -- 
> C. Balasubramanian
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