Executables

I.    To score a PDB file, and to get the profile scores
      and neighbor residues of each residue, use GetProfile.
      Details are given in the Readme file.
      Here is a sample profile output file for 2ACY.

      Download the appropriate executable as a binary file. The Readme file
      should also be saved into the same directory where the executable file is saved
      without the .txt extension.

      The default command looks like

 > GetProfile ../pdbs/1ERX.pdb A ../pdbs/profiles/profile_1ERX 
     The PDB file and the file to which the profile is to be written could be
     located somewhere else in the machine. As long as the full path is given,
     the codes should work fine.
     Please refer to the Readme file for details about additional options available.

II.   Virtual mutagenesis

III. To generate a new table of log-likelihood ratios using
       a list of PDB chains, use GetPot.
       Details are given in the Readme file.

       Download the appropriate executable as a binary file. The Readme file
       should also be saved into the same directory where the executable file is saved
       without the .txt extension.

       The default command looks like

 > GetPot list_pdbs ../PotTables/Table4B_SC.dat 

Bala Krishnamoorthy
Last modified: Tue Apr 3 16:59:34 PDT 2007