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Matt<br>
<br>
<br>
<blockquote
cite="mid:19aa7d860810230310g42686d4v3b8e0e3abcd1b8c0@mail.gmail.com"
type="cite">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?<br>
</blockquote>
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
correct. It also adds hydrogens among other things.<br>
<blockquote
cite="mid:19aa7d860810230310g42686d4v3b8e0e3abcd1b8c0@mail.gmail.com"
type="cite">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<font size="2">: phenix.elbow input_file.pdb --add-hydrogens=True,
and I can't find this option under the elbow manual?<br>
And actually I would like to remove those hydrogens so it should be
"add-hydrogens=false"? I am now using </font>phenix-1.3-rc2. <br>
</blockquote>
<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.
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.<br>
<br>
Nigel<br>
<pre class="moz-signature" cols="72">--
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 : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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