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 ----------------------------------------------------------------------------