DB_average (170114)

Db_average <mol> <atom property>


This command allows one to calculate the average of an atom property over a range of selected atoms. The default property is the atomic temperature factor.

Here I evaluate the average temperature factor of the atoms in the PDB entry 3AUA:


 O > Db_average

 New> Average the atom-based property of the selected atoms

 New> Molecule [QQQ   ]:3aua

 New> Atom-based ODB 3aua_atom_[B]:

 New> Alternates will be used in the calculation.

 New> Average is 26.480 over 7076 atoms.


Although no selection was explicitly made, after reading in a PDB set of coordinates, all atoms are set to have their selection proper ON. The average is, therefore, taken over all atoms in the molecule.

This data set is an enzyme-inhibitor complex and contains the antibiotic FR-900098, which is the acetyl analogue of fosmidomycin. If we want to obtain the average temperature factor for just the inhibitor that is found in the A-chain of 3AUA (residue A701), we would need to set up the correct selection properties:


 O > mol 3aua

 O > sel_off

 Sel> What molecule [3AUA  ]:

 Sel> Residue range [all molecule]:

 O > sel_on 

 Sel> What molecule [3AUA  ]:

 Sel> Residue range [all molecule]:a701 a701

 O > Db_average

 New> Average the atom-based property of the selected atoms

 New> Molecule [3AUA  ]:

 New> Atom-based ODB 3aua_atom_[B]:

 New> Alternates will be used in the calculation.

 New> Average is 20.806 over 14 atoms.


In the above, all atoms are first set OFF, and then the atoms in the desired residue are set ON, before calculating the average.