[phenixbb] phenix.autobuild

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Oct 23 08:37:10 PDT 2008


> 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 


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 : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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