Hi,<div><br></div><div>Please help me if possible, I have been stuck few days by now :-(</div><div><br></div><div>I am trying a very basic approach to use modeller, but in this case I am using my own global alignment from clustalW.  I am trying a very basic protein, target: 1aho, and only one template 2kbh_A</div>

<div><br></div><div>ClustalW outputs the alignment in PIR format (<a href="http://www.bioinformatics.nl/tools/crab_pir.html" target="_blank">http://www.bioinformatics.nl/tools/crab_pir.html</a>) but is a different PIR format than the one required by modeller.  Actually the main difference is that clustalW does not provide the <span style="font-family:monospace;font-size:medium;white-space:pre"><em>start residue</em>:<em>start chain code</em>:<em>end<span style="font-style:normal"><em> residue</em>:<em>end chain code</em>:<span style="font-size:small"><font face="arial, helvetica, sans-serif"> parts.</font></span></span></em></span></div>


<div><font face="arial, helvetica, sans-serif"><span style="white-space:pre"><br></span></font></div><div><font face="arial, helvetica, sans-serif"><span style="white-space:pre">I do not know how to get that information and modeller apparently does not know either.  Here I copy and paste the clustalW PIR format, the PIR modeller format and the errors I get from the model_simple.log.</span></font></div>


<div><font face="arial, helvetica, sans-serif"><span style="white-space:pre"><br></span></font></div><div><font face="arial, helvetica, sans-serif"><span style="white-space:pre"><b>CLUSTALW PIR format - sequencealn.pir</b></span></font></div>

<div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><span class="Apple-style-span" style="white-space: pre;"><br></span></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><span class="Apple-style-span" style="white-space: pre;"><div>

&gt;P1;1AHO_A|PDBID|CHAIN|SEQUENCE</div><div><br></div><div>VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK</div><div>LPDHVRTKGPGRCH--</div><div>*</div><div>&gt;P1;2KBH_A|PDBID|CHAIN|SEQUENCE</div><div><br></div><div>
VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK</div>
<div>LPDDARIMKPGRCNGG</div><div>*</div><div><br></div></span></font></div>

<div><b>MODELLER INPUT (does not work, not sure why)</b></div><div><br></div><div><div>&gt;P1;1aho</div><div>sequence:1aho:     : :     : ::: 0.00: 0.0</div><div>VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK</div><div>

LPDHVRTKGPGRCH--*</div><div><br></div><div>&gt;P1;2kbhA</div><div>structureX:2kbh.pdb:     : :     : ::: 0.00: 0.0</div><div>VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK</div><div>LPDDARIMKPGRCNGG*</div><div><br></div>

<div><b>ERROR MODELLER GIVES ME:</b></div><div><br></div><div><div>get_ran_648E&gt; Alignment sequence not found in PDB file:        1  2kbh.pdb</div><div>              (You didn&#39;t specify the starting and ending residue numbers and</div>

<div>              chain IDs in the alignment, so Modeller tried to guess these fr</div><div>              the PDB file.)</div><div>              Suggestion: put in the residue numbers and chain IDs (see the</div><div>              manual) and run again for more detailed diagnostics.</div>

<div>              You could also try running with allow_alternates=True to accept</div><div>              alternate one-letter code matches (e.g. B to N, Z to Q).</div><div>Traceback (most recent call last):</div><div>  File &quot;hoModeller-clustalaln.py&quot;, line 14, in &lt;module&gt;</div>

<div>    a.make()          # do the homollogy modelling</div><div>  File &quot;/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py&quot;, line 98,</div><div>    self.homcsr(exit_stage)</div><div>  File &quot;/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py&quot;, line 411,</div>

<div>    aln = self.read_alignment()</div><div>  File &quot;/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py&quot;, line 401,</div><div>    aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])</div>

<div>  File &quot;/n/sw/modeller-9v7/modlib/modeller/alignment.py&quot;, line 79, in append</div><div>    allow_alternates)</div><div>_modeller.SequenceMismatchError: get_ran_648E&gt; Alignment sequence not found i</div>
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</div><div><br></div><div>I am aware that the error advice me to put the start and ending residues numbers but I am still not sure how to solve the issue.</div><div><br></div><div>Any help will be strongly appreciated, I need to use modeller as soon as possible to do some progress in my research.</div>

<div><br></div><div>Best,</div><div><div><div><br>-- <br>Daniel F.<br><br>Department of Statistics, Harvard University<br>
1 Oxford Street, Cambridge, MA 02138<br>
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