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
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*