Re: [modeller_usage] ERROR ALIGN_CODES

23 Oct 2009


      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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Skickat: den 23 oktober 2009 08:42
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Today's Topics:
1. ERROR ALIGN_CODES (Leonardo Herrera)
----------------------------------------------------------------------
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

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