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Further to Ian's comments, there is also a schematic diagram of the accessible surface area (versus the molecular surface) in a CCP4 newsletter article about AREAIMOL and SURFACE (#38, April 2000) (the molecular surface is different from the solvent accessible surface as it is smoothly varying between atoms, whereas the solvent accessible surface has sharp "dents"). I don't know whether anyone quotes the contact area however - generally it seems that the ASA is sufficient. Contact area calculation was implemented in AREAIMOL mainly in order to match similar functionality in the SURFACE program. Hope this helps, best wishes Peter On Wed, 28 Sep 2005 [EMAIL PROTECTED] wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > Hello, > > I recently started using 'areaimol' in the CCP4 program suite, > > CCP4 5.0 > AREAIMOL 5.0 > 30/01/04 > > I am using default settings to look at 'simple area calculation' of a > protein. The results file has two major sections, > > 1) ACCESSIBLE AREAS (for the residue/chain/oligomer) > 2) CONTACT AREAS (for the residue/chain/oligomer) > > What is the difference between these two measures? (Are they even related > measures, or do they measure different physical properties of the > molecule?) > > >From the manual I read... > > "The contact area is defined as the area on the Van der Waals surface of > an atom that can be contacted by a sphere of the given probe radius." > > but that sounds just like the ASA? > > I am a beginner with these concepts, so I don't see how (if at all) the > two measures are related, or why two measures are needed. > > Thanks for any help, > > Dan. > > > > > -- _____________________________________________________ Peter J Briggs, [EMAIL PROTECTED] Tel: +44 1925 603826 CCP4, [EMAIL PROTECTED] Fax: +44 1925 603825 http://www.ccp4.ac.uk/ Daresbury Laboratory, Daresbury, Warrington WA4 4AD
