Actually, after I change Zn to ZN, phenix.elbow does not work with the following error message:<br>phenix.elbow overall_best_090909e_001-coot-0.pdb --all-residues --do-all<br> ------------------------------------------------------------------------------<br>
  electronic Ligand Builder &amp; Optimisation Workbench (eLBOW) 1.4 3<br>    - Nigel W. Moriarty (NWMoriarty@LBL.Gov)<br> ------------------------------------------------------------------------------<br><br> Random number seed:  1653885000<br>
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P<br><br>        No unknown residues<br>[qwan@phaser2 AutoBuild_run_10_]$ phenix.elbow overall_best_090909e_001-coot-0.pdb               ------------------------------------------------------------------------------<br>
  electronic Ligand Builder &amp; Optimisation Workbench (eLBOW) 1.4 3<br>    - Nigel W. Moriarty (NWMoriarty@LBL.Gov)<br> ------------------------------------------------------------------------------<br><br> Random number seed:  1654559024<br>
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P<br><br>        No molecule read<br><br>        Use --all-residues to view residues if this is a PDB file<br><br><br><div class="gmail_quote">
On Fri, Sep 11, 2009 at 7:19 PM, Pavel Afonine <span dir="ltr">&lt;<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">



  

<div bgcolor="#ffffff" text="#000000">
Yes, the capitalization matters. Ralf is notified.<br>
Pavel.<div><div></div><div class="h5"><br>
<br>
<br>
On 9/11/09 4:08 PM, Nathaniel Echols wrote:
</div></div><blockquote type="cite"><div><div></div><div class="h5">
  <pre>On Sep 11, 2009, at 3:54 PM, Pavel Afonine wrote:
  </pre>
  <blockquote type="cite">
    <blockquote type="cite">
      <pre>I have Zn atoms in my pdb for refinement. However, it failed with  
the following scripts. Do I have to create a libary of this heavy  
atom?
      </pre>
    </blockquote>
    <pre>no, you shouldn&#39;t. Zn should be recognized automatically if it is  
properly defined in input PDB file. I just verified that if it is  
formatted like this:

HETATM 2306 ZN    ZN D   1      24.598  75.945  -1.390  1.00   
5.00          ZN

then it works fine. I&#39;m not sure if capitalization is important as  
well as HETATM instead of ATOM - this is something you can try in no  
time.
    </pre>
  </blockquote>
  </div></div><pre><div><div></div><div class="h5">

I&#39;m pretty sure capitalization is indeed important, because I had a  
similar problem in both phenix.refine and eLBOW with manganese (MN is  
okay, Mn is not).

-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
<a href="mailto:NEchols@lbl.gov" target="_blank">NEchols@lbl.gov</a></div></div>



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</blockquote>
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