[phenixbb] phenix.autobuild
Nigel W Moriarty
NWMoriarty at lbl.gov
Thu Oct 23 08:37:10 PDT 2008
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 : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20081023/e20815b6/attachment-0003.htm>
More information about the phenixbb
mailing list