[phenixbb] phenix.autobuild

Matthew Chu linghonmatthew at gmail.com
Thu Oct 23 03:10:59 PDT 2008

Thank you for the detailed information Tom, my autobuild job is actually
running properly!

Just some more minors questions:
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?
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't
work: phenix.elbow input_file.pdb --add-hydrogens=True, and I can't find
this option under the elbow manual?
And actually I would like to remove those hydrogens so it should be
"add-hydrogens=false"? I am now using phenix-1.3-rc2.
Thanks again!


Matthew LH Chu
PhD Student
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
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