Hi Matt, I recommend updating to the latest version of PHENIX (1.3 final) from the web page. Cheers, Paul On Oct 23, 2008, at 3:10 AM, Matthew Chu wrote:

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!

Matt

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

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-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Kristine Sawyer [ [email protected] ][ 1-510-486-4151 ] --

Thanks Nigel. The CIF files generated by SKETCHER in ccp4i work fine in both phenix.refine and refmac, but seems they don't work in phenix.autobuild....(they should work the same right?) I am not sure why, but I will try what you suggested. Thank you so much again! Matt 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.

* 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.

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. * 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 http://www.phenix-online.org/mailman/listinfo/phenixbb Web : CCI.LBL.gov -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------