How to compute contact surface with Xplor

Alexandre Bonvin abonvin at PANDA.CHEM.UU.NL
Wed Nov 3 08:57:58 EST 1999


>
>Hi all 
>
>In my current project I want to compute the surface area
>of a molecule buried by an intermolecular interaction.
>But I didn't find the method in detail in Xplor or other
>reference.  

Here is an example for a protein-DNA complex:


{====>}				        {* solvant accessible surface *}
surface mode=access rh2o=1.4 sele=(segid PROT or segid DNA*) end
vector show sum (rmsd) (segid PROT or segid DNA*)
evaluate ($saac = $result)
surface mode=access rh2o=1.4 sele=(segid PROT) end
vector show sum (rmsd) (segid PROT)
evaluate ($saap = $result)
surface mode=access rh2o=1.4 sele=(segid DNA*) end
vector show sum (rmsd) (segid DNA*)
evaluate ($saad = $result)
evaluate ($saab = $saap + $saad - $saac)

i.e.: 
 1) calculate the saa of the protein only
 2) calculate the saa of the dna only
 3) calculate the saa of the protein-dna complex
 4) buried saa = 1 + 2 - 3

Cheers,
Alexandre

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