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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users