Re: [ccp4bb]: about areaimol

["P.J.Briggs" <P.J.Briggs@dl.ac.uk>]

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Dear Xu Zhen

I'm not that the "cavity" stuff is what you need ... in fact I think the
simplest way to calculate the buried area is unfortunately to run the
program twice, as follows:

1. Input pdb file with just the monomer, to get the accessible surface
area (ASA) for that component, say A1, then

2. Input pdb file with the dimer, to get the ASA for that, say A2.

The buried area will then be the difference in ASA between two monomers
compared with the dimer, i.e.

  A_diff = 2*A1 - A2

which I'm afraid needs to be calculated by hand. It is one of Areaimol's
shortcomings that this calculation is not currently implemented as a
single function.

Hope this helps, please get back in touch if this isn't what you
wanted to know.
Best wishes

Peter.

On Wed, 27 Nov 2002, xu zhen wrote:

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> 
> Hi,all,
> I am so sorry that this question is still about of the buried surface and 
> the surface of the dimer because I can't find the difference of the surface 
> area of the dimer and the sum of the two monomer in the log file of 
> areaimol.
> 
> As it mentioned in the manual of areaimol that "Multiple isolated surfaces 
> could represent any combination of 1.cavities within a single molecule, 2. 
> .....",does it mean when we think the dimer as a single molecule the 
> cavity--isolated surface is represent as the buried surface of the two 
> monomer?
> 
> 
> Best wishes
> Xu zhen
> 
> 
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--
_____________________________________________________
Peter J Briggs, pjx@ccp4.ac.uk   Tel: +44 1925 603826
CCP4,           ccp4@ccp4.ac.uk  Fax: +44 1925 603825
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Daresbury Laboratory, Daresbury, Warrington   WA4 4AD