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<p style="margin-bottom: 0in; font-family: courier new,monospace;">modeller  user&#39;s 
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<p style="margin-bottom: 0in; font-family: courier new,monospace;">I have a problem when I am realising 
my model with multiple templates, in the step to align the alignment
of pdb&#39;s versus my sequence I obtain the following problem…</p>
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<p style="margin-bottom: 0in; font-family: courier new,monospace;">Traceback (most recent call last):<br>  File &quot;align2d_mult.py&quot;, line 14, in &lt;module&gt;<br>    aln.append(file=&#39;Tc30.ali&#39;, align_codes=&#39;giAAR00925&#39;)<br>
  File &quot;/usr/lib/python2.6/site-packages/modeller/alignment.py&quot;, line 79, in append<br>    allow_alternates)<br>_modeller.ModellerError: read_al_373E&gt; Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(      13) =  giAAR00925<br>
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<p style="margin-bottom: 0in; font-family: courier new,monospace;">I could&#39;nt find an answer to this
problem, it already changes the format (fasta to pir ...), and code
several times (giAAR00925 to 13... to c30 ...), so please can
somebody help with this error message?</p><p style="margin-bottom: 0in; font-family: courier new,monospace;">thanks in advance 
</p>
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<p style="margin-bottom: 0in; font-family: courier new,monospace;">My script is 
</p>
<p style="margin-bottom: 0in; font-family: courier new,monospace;">from modeller import *<br>log.verbose()<br>env = environ()<br>env.libs.topology.read(file=&#39;$(LIB)/top_heav.lib&#39;)<br><br># Read aligned structure(s):<br>
aln = alignment(env)<br>aln.append(file=&#39;alineamiento.ali&#39;, align_codes=&#39;all&#39;)<br>aln_block = len(aln)<br><br># Read aligned sequence(s):<br>aln.append(file=&#39;Tc30.ali&#39;, align_codes=&#39;giAAR00925&#39;)<br>
<br># Structure sensitive variable gap penalty sequence-sequence alignment:<br>aln.salign(output=&#39;&#39;, max_gap_length=20,<br>           gap_function=True,   # to use structure-dependent gap penalty<br>           alignment_type=&#39;PAIRWISE&#39;, align_block=aln_block,<br>
           feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0,<br>           gap_penalties_1d=(-450, 0),<br>           gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.),<br>           similarity_flag=True)<br>
<br>aln.write(file=&#39;Tc30-mult.ali&#39;, alignment_format=&#39;PIR&#39;)<br>aln.write(file=&#39;Tc30-mult.pap&#39;, alignment_format=&#39;PAP&#39;)</p><p style="margin-bottom: 0in; font-family: courier new,monospace;">
<br></p><p style="margin-bottom: 0in; font-family: courier new,monospace;">my Tc30.ali is<br style="font-family: courier new,monospace;"></p><span style="font-family: courier new,monospace;"><br>giAAR00925  524 residues</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">MGRLQRFSAFVPLTLSFISQASAAIGPVTDLTISDADISPDGFTRAAVVMNDQFPGPLIAGNKGDNFQINVI</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">DNLSNSTMLTSTTIHWHGFFQKGTNWADGAAFVNQCPISAGNSFLYDFTATDQAGTFWYHSHLSTQYCDGLR</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">GPMVVYDPDDPHASLYDVDDDSTVITLSDWYHTAARLGARFPAGADSTLINGLGRAAGGDADAALAVFNVTQ</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">GSRYRFRLVSLSCDPNFNFTIQDHNMTIIEVDGVNVEPVTVDSIQIFAGQRYSFVLTADQDIGNYWIQAVPN</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">TGTVTTDGGVNSAILRYDTADPIEPDAADPTSSIPLVETDLVPLENLAAPGDPTVGGVDLAMNLEFDFNGTW</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">FFINGEPFVPPSVPVLLQIMSGAQSAADLLPSGSVYTLPANSTIEISFPMNTTAAPGAPHPFHLHGHTFYVV</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">RSAGSTEYNYVNPPQRDTVSTGTDGDNVTIRFTTNNPGPWFLHCHIDFHLDAGFAIVLSEDTPDAASANTPS</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">SAWDDLCPTYNTDYPDGLGR*</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><p style="margin-bottom: 0in; font-family: courier new,monospace;">and my alineamiento.ali is</p>
<p style="margin-bottom: 0in; font-family: courier new,monospace;">&gt;P1;1gw0.10wA<br>structureX:1gw0.10w_fit.pdb:   1 :A:+573 :A:::-1.00:-1.00<br>--EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANW<br>
GDTVEVTVINNLV----TNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRAR-QYGTSWYHSHFSA<br>QYGNGVVGTIQING---PASLPYDID--LGVFPITDYYYRAADDLVHFTQN-----NAPPFSDNVLINGTAVNPN<br>TGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAP<br>
-DNYWFNVTFGGQAACGG-----SLNPH----PAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSV--<br>PVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGN------TSYPVSDNIVQVDAVDQWT<br>YWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQ-RFVFDPAVDLARLNGDNPPRRDTTMLPAG---GW<br>
LLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL--<br>----------------------....wwwwwwwwww*<br><br>&gt;P1;1gyc.10wA<br>structureX:1gyc.10w_fit.pdb:   1 :A:+513 :A:::-1.00:-1.00<br>AI--------------------------------GPAASLVVANA--PVSPDG-FLRDAIVVNGVFPSPLITGKK<br>
GDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIAS-GHSFLYDFHVPDQAGTFWYHSHLST<br>QYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPR----------FPLGADATLINGLGRSAS<br>TPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTV<br>
-GNYWIRANPN--F---------GTVGFAGGINSAILRYQGAPVAEPTTTQTTS-VIP-LIETNLHPLARMPVPG<br>SPTPGGVDKALNLAFNFNG-----TNFFINNASFTPP-TVPVLLQILSG---AQTAQDLLPAGSVYPLP-AHSTI<br>EITLPATA-LAPGAPHPFHLHGHAFAVVRSAGS----------------T--TYNYNDPIFRDVVSTGTPAAGDN<br>
VTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAA--NPVPKAWSDLCPIYDGLSEANQ----------<br>----------------------....wwwwwwwwww*<br><br>&gt;P1;1kya.10wA<br>structureX:1kya.10w_fit.pdb:   1 :A:+513 :A:::-1.00:-1.00<br>GI--------------------------------GPVADLTITNA--AVSPDG-FSRQAVVVNGGTPGPLITGNM<br>
GDRFQLNVIDNLTNHTMLKSTSIHWHGFFQKGTNWADGPAFINQCPISS-GHSFLYDFQVPDQAGTFWYHSHLST<br>QYCDGLRGPFVVYDPNDPAADLYDVDNDDTVITLVDWYHVAAKLGPA----------FPLGADATLINGKGRSPS<br>TTTADLSVISVTPGKRYRFRLVSLSCDPNYTFSIDGHNMTIIETDSINTAPLVVDSIQIFAAQRYSFVLEANQAV<br>
-DNYWIRANPN--F---------GNVGFTGGINSAILRYDGAAAVEPTTTQTTS-TAP-LNEVNLHPLVATAVPG<br>SPVAGGVDLAINMAFNFNG-----TNFFINGASFTPP-TVPVLLQIISG---AQNAQDLLPSGSVYSLP-SNADI<br>EISFPATA-AAPGAPHPFHLHGHAFAVVRSAGS----------------T--VYNYDNPIFRDVVSTGTPAAGDN<br>
VTIRFRTDNPGPWFLHCHIDFHLEAGFAVVFAEDIPDVASA--NPVPQAWSDLCPTYDARDPSDQ----------<br>----------------------....wwwwwwwwww*<br><br>
</p><br style="font-family: courier new,monospace;"><p style="margin-bottom: 0in; font-family: courier new,monospace;"><br>
</p>
<br style="font-family: courier new,monospace;" clear="all"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">-- </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">MenB Leonardo David Herrera Zúñiga</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">POSGRADO EN QUÍMICA  UAMI Biofisicoquímica</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Universidad Autonoma Metropolitana Iztapalapa</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Tel. +52 (55) 5804 4674  </span><br>