Re: [ccp4bb]: Molecular surface calculation

[Jon Agirre]

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi, you may want to give Oleg Tsodikov's 'Surface Racer' a try. You can get binaries at http://monte.biochem.wisc.edu/~tsodikov/surface.html Good luck! Best regards, Jon Erwin De Genst wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** 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. -- ******************************** Jon Agirre Hernández Unidad de Biofisica (CSIC-UPV/EHU) P.O.Box 644, E-48080 Bilbao, Spain. Blog: http://lostsymmetry.blogspot.com Web: http://www.ehu.es/biofisica E-mail: [EMAIL PROTECTED] Tel: +34 94 601 3345 Fax: +34 94 601 3360