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<p class="MsoNormal"><span style="font-size:11.0pt">Hi, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am trying to make a comparative model using modeler. I downloaded my sequence from uniprot and a homolog protein from the pdb. I associated the sequence with the homologe and the alignment is okay however
there are definitely regions where there is no match at all. So when I run modeler it fails with the following output:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./6opc_1.pdb<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">(You didn't specify the starting and ending residue numbers and<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">chain IDs in the alignment, so Modeller tried to guess these from<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">the PDB file.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Suggestion: put in the residue numbers and chain IDs (see the<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">manual) and run again for more detailed diagnostics.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">You could also try running with allow_alternates=True to accept<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">alternate one-letter code matches (e.g. B to N, Z to Q).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have been trying to figure out how exactly to specify the chain IDs and residue numbers but I really didn’t get it. May I ask you to provide an example please?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">David<o:p></o:p></span></p>
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