Hello Leonardo

My first guess would be that the Tc30.ali file is impossible for Modeller to interpret. In the tutorial example the .ali file has the following format:

>P1;TvLDH sequence:TvLDH:::::::0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWI...

But then again you say that you have tried the PIR format. However, the error message implies that it cannot read the sequence for giAAR00925. Have you tried to just change the Tc30.ali file to:

>P1;giAAR00925 sequence:giAAR00925:::::::0.00: 0.00 MGRLQRFSAFVPLTLSF...

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Today's Topics:

1. ERROR ALIGN_CODES (Leonardo Herrera)

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Message: 1 Date: Thu, 22 Oct 2009 23:42:04 -0700 From: Leonardo Herrera ldhz04@yahoo.com.mx To: modeller_usage@salilab.org Subject: [modeller_usage] ERROR ALIGN_CODES Message-ID: 18c41c7f0910222342g41b9c28eq848322c47110f8d9@mail.gmail.com Content-Type: text/plain; charset="windows-1252"

Hi

modeller user's

I have a problem when I am realising my model with multiple templates, in the step to align the alignment of pdb's versus my sequence I obtain the following problem?

Traceback (most recent call last): File "align2d_mult.py", line 14, in <module> aln.append(file='Tc30.ali', align_codes='giAAR00925') File "/usr/lib/python2.6/site-packages/modeller/alignment.py", line 79, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 13) = giAAR00925

I could'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?

thanks in advance

My script is

from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib')

# Read aligned structure(s): aln = alignment(env) aln.append(file='alineamiento.ali', align_codes='all') aln_block = len(aln)

# Read aligned sequence(s): aln.append(file='Tc30.ali', align_codes='giAAR00925')

# Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(output='', max_gap_length=20, gap_function=True, # to use structure-dependent gap penalty alignment_type='PAIRWISE', align_block=aln_block, feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0, gap_penalties_1d=(-450, 0), gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.), similarity_flag=True)

aln.write(file='Tc30-mult.ali', alignment_format='PIR') aln.write(file='Tc30-mult.pap', alignment_format='PAP')

my Tc30.ali is

giAAR00925 524 residues MGRLQRFSAFVPLTLSFISQASAAIGPVTDLTISDADISPDGFTRAAVVMNDQFPGPLIAGNKGDNFQINVI DNLSNSTMLTSTTIHWHGFFQKGTNWADGAAFVNQCPISAGNSFLYDFTATDQAGTFWYHSHLSTQYCDGLR GPMVVYDPDDPHASLYDVDDDSTVITLSDWYHTAARLGARFPAGADSTLINGLGRAAGGDADAALAVFNVTQ GSRYRFRLVSLSCDPNFNFTIQDHNMTIIEVDGVNVEPVTVDSIQIFAGQRYSFVLTADQDIGNYWIQAVPN TGTVTTDGGVNSAILRYDTADPIEPDAADPTSSIPLVETDLVPLENLAAPGDPTVGGVDLAMNLEFDFNGTW FFINGEPFVPPSVPVLLQIMSGAQSAADLLPSGSVYTLPANSTIEISFPMNTTAAPGAPHPFHLHGHTFYVV RSAGSTEYNYVNPPQRDTVSTGTDGDNVTIRFTTNNPGPWFLHCHIDFHLDAGFAIVLSEDTPDAASANTPS SAWDDLCPTYNTDYPDGLGR*

and my alineamiento.ali is

>P1;1gw0.10wA structureX:1gw0.10w_fit.pdb: 1 :A:+573 :A:::-1.00:-1.00 --EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANW GDTVEVTVINNLV----TNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRAR-QYGTSWYHSHFSA QYGNGVVGTIQING---PASLPYDID--LGVFPITDYYYRAADDLVHFTQN-----NAPPFSDNVLINGTAVNPN TGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAP -DNYWFNVTFGGQAACGG-----SLNPH----PAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSV-- PVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGN------TSYPVSDNIVQVDAVDQWT YWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQ-RFVFDPAVDLARLNGDNPPRRDTTMLPAG---GW LLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL-- ----------------------....wwwwwwwwww*

>P1;1gyc.10wA structureX:1gyc.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 AI--------------------------------GPAASLVVANA--PVSPDG-FLRDAIVVNGVFPSPLITGKK GDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIAS-GHSFLYDFHVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPR----------FPLGADATLINGLGRSAS TPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTV -GNYWIRANPN--F---------GTVGFAGGINSAILRYQGAPVAEPTTTQTTS-VIP-LIETNLHPLARMPVPG SPTPGGVDKALNLAFNFNG-----TNFFINNASFTPP-TVPVLLQILSG---AQTAQDLLPAGSVYPLP-AHSTI EITLPATA-LAPGAPHPFHLHGHAFAVVRSAGS----------------T--TYNYNDPIFRDVVSTGTPAAGDN VTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAA--NPVPKAWSDLCPIYDGLSEANQ---------- ----------------------....wwwwwwwwww*

>P1;1kya.10wA structureX:1kya.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 GI--------------------------------GPVADLTITNA--AVSPDG-FSRQAVVVNGGTPGPLITGNM GDRFQLNVIDNLTNHTMLKSTSIHWHGFFQKGTNWADGPAFINQCPISS-GHSFLYDFQVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPNDPAADLYDVDNDDTVITLVDWYHVAAKLGPA----------FPLGADATLINGKGRSPS TTTADLSVISVTPGKRYRFRLVSLSCDPNYTFSIDGHNMTIIETDSINTAPLVVDSIQIFAAQRYSFVLEANQAV -DNYWIRANPN--F---------GNVGFTGGINSAILRYDGAAAVEPTTTQTTS-TAP-LNEVNLHPLVATAVPG SPVAGGVDLAINMAFNFNG-----TNFFINGASFTPP-TVPVLLQIISG---AQNAQDLLPSGSVYSLP-SNADI EISFPATA-AAPGAPHPFHLHGHAFAVVRSAGS----------------T--VYNYDNPIFRDVVSTGTPAAGDN VTIRFRTDNPGPWFLHCHIDFHLEAGFAVVFAEDIPDVASA--NPVPQAWSDLCPTYDARDPSDQ---------- ----------------------....wwwwwwwwww*

-- MenB Leonardo David Herrera Z??iga POSGRADO EN QU?MICA UAMI Biofisicoqu?mica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674