Hi everyone,<div><br></div><div>I want to read in hydrogens, heteroatoms and water molecules into my modeller-modeled protein  structure. In the manual it says:</div><div><br></div><div> to read in the heteroatoms, put</div>
<div><br></div><div><font color="#000099">env.io.hetatm=true</font> and to use &#39;.&#39; characters in the alignment sequences. </div><div><br></div><div><div> to read in the waters, put</div><div><br></div><div><font color="#000099">env.io.water=true</font> and to use &#39;w&#39; characters in the alignment sequences. </div>
<br class="Apple-interchange-newline"></div><div><br></div><div>Usually in a pdb file the &#39;ligand&#39; heteroatoms are given as  HETATM  843 FE1  SF4 A 107      14.698  20.785  10.230  1.00 13.78          FE </div><div>
<br></div><div>and waters are given as                                                 HETATM  858  O   HOH A 109      23.833  10.228  18.799  1.00 17.80           O  </div><div><br></div><div>so both of them use &#39;HETATM&#39; . So my question is if we have asked the modeller to read ALL HETATM records by setting <font color="#000099">env.io.hetatm=true</font>, do we have to specifically </div>
<div><br></div><div>say again, to add waters by <font color="#000099">env.io.water=true</font>.  Can&#39;t we just read all the heteroatom records (including waters) and use &#39;.&#39; for both normal heteroatoms and waters?</div>
<div><br></div><div>Thank you</div><div><br></div><div>Sajeewa Dewage</div>