[Chimera-users] buriedArea calculation: MSMS vs Chimera

Bala subramanian bala.biophysics at gmail.com
Fri Apr 1 11:11:46 PDT 2016


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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