Thank you for the detailed information Tom, my autobuild job is actually running properly! <br><br>Just some more minors questions:<br>1. AutoBuild Wizard will use phenix.elbow to generate geometries for any
ligands that are not recognized, but how can I find out which ligands that can actually be recognized by phenix? Or to be save, we better run elbow to generate the libraries for every single ligands?<br>2. 


eLBOW can automatically add hydrogens to the input molecules if there are less
than a quarter of the possible hydrogens, however this command doesn&#39;t work<font size="2">: phenix.elbow input_file.pdb --add-hydrogens=True, and I can&#39;t find this option under the elbow manual?<br>And actually I would like to remove those hydrogens so it should be &quot;add-hydrogens=false&quot;? I am now using </font>phenix-1.3-rc2. <br>
Thanks again!<br><br>Matt<br><br><br>-- <br>----------------------------------------------------------------------------<br>Matthew LH Chu<br>PhD Student<br>School of Pharmacy and Pharmaceutical Sciences <br>University of Manchester<br>
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