Matt

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?

There are a number of tools available.

phenix.pdbtools file.pdb

will tell you if a PDB file has non-recognised ligands.

phenix.elbow --do-all model.pdb

will calculate all the ligands in the PDB file.

phenix.ready_set model.pdb

will calculate all the ligands and check that the atom names are correct. It also adds hydrogens among other things.

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.

To get an absolute list of the options you can

phenix.elbow --help

The --add-hydrogens options overwrites the automatic choice by eLBOW. If you don't want the hydrogens in your PDB and CIF files use --write-hydrogens=False. This arises because the internal representation must have the hydrogens for accurate geometries and restraints.

Nigel

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : [email protected]
Web   : CCI.LBL.gov