<div dir="ltr">Dear Pavel and others,<div><br></div><div>After looking through the files, I found that the error is due to the missing dna_rna cif files in the geostd folder.</div><div><br></div><div>mmtbx/monomer_library/pdb_interpretation.py calls to <br></div><div>mmtbx/monomer_library/server.py then read the structure information from geostd folder. <br></div><div><br></div><div>In the release I obtained from server using bootstrap.py, the information about chem_data was not downloaded (maybe it is in a different location?). </div><div><br></div><div>After copying a chem_data to modules, the program works fine.</div><div><br></div><div>Best,</div><div>Haiguang</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 30, 2017 at 11:35 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Haiguang,<br>
<br>
please send us PDB file and we will investigate.<br>
<br>
Thanks,<br>
Pavel<div><div class="h5"><br>
<br>
<div class="m_-844297623577922870moz-cite-prefix">On 8/30/17 07:23, Haiguang Liu wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Dear All,
<div><br>
</div>
<div>I recently run into an error while processing DNA molecules
using pdb_interpreter. The error message is as the following:</div>
<div><br>
</div>
<div>
<div> File
"/Users/hgliu/test/cctbx/<wbr>modules/cctbx_project/mmtbx/<wbr>monomer_library/pdb_<wbr>interpretation.py",
line 5419, in __init__</div>
<div> restraints_loading_flags=<wbr>restraints_loading_flags)</div>
<div> File
"/Users/hgliu/test/cctbx/<wbr>modules/cctbx_project/mmtbx/<wbr>monomer_library/pdb_<wbr>interpretation.py",
line 3221, in __init__</div>
<div> log=log,</div>
<div> File
"/Users/hgliu/test/cctbx/<wbr>modules/cctbx_project/mmtbx/<wbr>monomer_library/pdb_<wbr>interpretation.py",
line 2507, in __init__</div>
<div> m_j=mm,</div>
<div> File
"/Users/hgliu/test/cctbx/<wbr>modules/cctbx_project/mmtbx/<wbr>monomer_library/pdb_<wbr>interpretation.py",
line 1693, in get_lib_link</div>
<div> return mon_lib_srv.link_link_id_dict[<wbr>"rna3p"]</div>
<div>KeyError: 'rna3p'</div>
</div>
<div><br>
</div>
<div>After searching through the threads, I found the same error
has been reported, but no solution posted. Any suggestion is
appreciated.</div>
<div><br>
</div>
<div>Best,</div>
<div>haiguang</div>
</div>
<br>
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<br>
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</pre>
</blockquote>
<br>
</div>
</blockquote></div><br></div>