<pre><font size="4"><font face="arial,helvetica,sans-serif">Thanks Nigel. <br>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?)<br>
I am not sure why, but I will try what you suggested. Thank you so much again!<br><br>Matt<br> </font></font><br>
<br>Matt<br><br><br>><i> 1. AutoBuild Wizard will use phenix.elbow to generate geometries for <br></i>><i> any ligands that are not recognized, but how can I find out which <br></i>><i> ligands that can actually be recognized by phenix? Or to be save, we <br>
</i>><i> better run elbow to generate the libraries for every single ligands?<br></i>There are a number of tools available.<br><br>phenix.pdbtools file.pdb<br><br>will tell you if a PDB file has non-recognised ligands.<br>
<br>phenix.elbow --do-all model.pdb<br><br>will calculate all the ligands in the PDB file.<br><br>phenix.ready_set model.pdb<br><br>will calculate all the ligands and check that the atom names are <br>correct. It also adds hydrogens among other things.<br>
><i> 2. eLBOW can automatically add hydrogens to the input molecules if <br></i>><i> there are less than a quarter of the possible hydrogens, however this <br></i>><i> command doesn't work: phenix.elbow input_file.pdb <br>
</i>><i> --add-hydrogens=True, and I can't find this option under the elbow manual?<br></i>><i> And actually I would like to remove those hydrogens so it should be <br></i>><i> "add-hydrogens=false"? I am now using phenix-1.3-rc2.<br>
</i><br>To get an absolute list of the options you can<br><br>phenix.elbow --help<br><br>The --add-hydrogens options overwrites the automatic choice by eLBOW. <br>If you don't want the hydrogens in your PDB and CIF files use <br>
--write-hydrogens=False. This arises because the internal <br>representation must have the hydrogens for accurate geometries and <br>restraints.<br><br>Nigel<br><br>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709<br>Fax : 510-486-5909<br>Email : <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">NWMoriarty at LBL.gov</a><br>
Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a><br>
</pre><br clear="all"><br>-- <br>----------------------------------------------------------------------------<br>Matthew LH Chu<br>PhD Student<br>School of Pharmacy and Pharmaceutical Sciences <br>University of Manchester<br>
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