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Hello Maher,<br>
<br>
this means your PDB file contains a molecule that cannot be matched
against known molecules in Phenix dictionary. Can you please send me
PDB file and I will be able to tell more.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/3/14 10:55 AM, maher alayyoubi
wrote:<br>
</div>
<blockquote
cite="mid:1951086978.4538282.1417632914323.JavaMail.yahoo@jws10645.mail.bf1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">Hi Everyone,</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">I am having
a problem of phenix.refine not accepting a pdb file that I
just finished editing in coot. It is a protein RNA compplex
where the protein part was built in buccaneer and the RNA
strand built in nautilus. I assembled the final model by text
editing the pdb file and adding the RNA part.</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">Whenever I
feed this pdb file into phenix, it comes back with two errors:
" number of atoms with unknown unbonded energy type symbols:6"
. "The coot command could not be located"</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">Does anyone
know how to fix this problem?</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">I tried
converting the file into mmcif and feeding it to phenix but
the same error comes back again.</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">Thank you
very much,</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr"><br>
</div>
<div id="yui_3_16_0_1_1417632428051_5117" dir="ltr">Maher<br>
</div>
</div>
</blockquote>
<br>
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