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Dear Sabine To maybe clarify slightly further what Guillaume refers to, in the newsletter article figure 2 the contact area for each atom is the area of that part of the molcular surface that is directly associated with that atom (i.e. the dashed lines that lie on the circles). It doesn't include the "reentrant" parts (i.e. the inwardly-curving parts that don't belong to any grey sphere). I hope this helps - I agree that the explanation in the documentation is pretty obtuse, I'll add some figures to the documentation itself to explain things better. Best wishes Peter On Wed, 29 Mar 2006, evrard wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Sabine Schneider wrote: > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Hi everyone, > > > > I am using areaimol to compare surface differences between a ligand-bound > > and apo structure, > > but I don't really understand the meaning of the "contact area" it is > > writting out. > > (the definition given in the program discription on the CCP4 website > > doesn't help me, sorry) > > > > Thanks a lot in advance! > > > > Sabine > > > > > > > > > > > > > > This message has been checked for viruses but the contents of an attachment > > may still contain software viruses, which could damage your computer system: > > you are advised to perform your own checks. Email communications with the > > University of Nottingham may be monitored as permitted by UK legislation. > > > > > > > > > Hi Sabine, > > You can have a look at the following CCP4 newsletter: > http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html > Fig. 1 shows how the solvent accessible surface area is defined > Fig. 2 shows what the contact area is. > > Guillaume > > -- > ****************************** > Guillaume Evrard > European Molecular Biology Laboratory, > Building 25A, room 309, > DESY, Notkestrasse 85, > 22603 Hamburg > Germany > > Phone:+49 (0) 40 89902 204 > Fax: +49 (0) 40 89902 149 > E-mail: [EMAIL PROTECTED] > ******************************** > > -- ___________________________________________________ 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
