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Summary: Liz's idea with mg works, and the baveraging can be done with a simple XL spreadsheet, and baverage in ccp4i works as well. However, my question was ill defined: Surface exposed is a contemptuous term. I actually meant 'solvent exposed in crystal structure'. This would mean that this value is not necessarily the same for same protein in different packing environments. This is not exactly trivial, and emphasizes the need for users of molecular models to understand and look at packing effects. Many others and myself have pointed this out repeatedly, to limited avail, I must admit...... With regards, br -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Liz Potterton Sent: Wednesday, October 11, 2006 3:40 AM To: [EMAIL PROTECTED] Cc: [email protected] Subject: Re: [ccp4bb]: surface residue average B *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi Bernhard, You can use CCP4mg to select the residues with solvent accessibility greater than whatever you choose for a cutoff. To do this pick 'Property' from the selection menu then in the new window set the property menu to 'residue SAS' and enter your required range. Then write the selected atoms to a PDB file (from the display object menu pick 'List selected atoms'). >From there I'm afraid you'll have to use a script to read the pdb and average the B values. Liz On Wednesday 11 October 2006 00:15, Bernhard Rupp wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Dear All, > > I am trying to find a program/script/procedure that allows me to > get an average B of the surface exposed residues. > Grateful for suggestions. > Thx, br > -------------------------------------------- > Bernhard Rupp, FRS > www.ruppweb.org > --------------------------------------------
