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Hi, I was following this discussion with interest since I am desperately looking for a program that calculates molecular surfaces. As I understand it 'areaimol' or 'surface' cannot calculate this because they do not calculate completely the surface described by the locus of the inward-facing probe sphere (the reentrant surface is lacking). Does anyone know if there is a program that calculates molecular surfaces and which gives an output per residue? Erwin > >Thanks all for your helpful replies. > >I found the article mentioned very useful, > >http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html > > >My major problems started when I confused the 'contact area' with the >'area in contact' for a subunit in an oligomer, but now I understand >that areaimol doesn't compute that directly. It would be really nice if >the man page for areaimol pointed to the above article. > >Cheers, >Dan. > > > >[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. >> >> >> >> > > > >
