[modeller_usage] Reading in water residues

[Sajeewa Pemasinghe <>]

Hi everyone,

I want to read in hydrogens, heteroatoms and water molecules into my modeller-modeled protein  structure. In the manual it says:

 to read in the heteroatoms, put

env.io.hetatm=true and to use '.' characters in the alignment sequences. 

 to read in the waters, put

env.io.water=true and to use 'w' characters in the alignment sequences. 

Usually in a pdb file the 'ligand' heteroatoms are given as  HETATM  843 FE1  SF4 A 107      14.698  20.785  10.230  1.00 13.78          FE 

and waters are given as                                                 HETATM  858  O   HOH A 109      23.833  10.228  18.799  1.00 17.80           O  

so both of them use 'HETATM' . So my question is if we have asked the modeller to read ALL HETATM records by setting env.io.hetatm=true, do we have to specifically 

say again, to add waters by env.io.water=true.  Can't we just read all the heteroatom records (including waters) and use '.' for both normal heteroatoms and waters?

Thank you

Sajeewa Dewage