I have errors in the build_profile() command, plx help me! - modeller_usage

1 Aug 2006


      I'm reading the basic tutorial and practicing to model my own protein.
My protein sequence is in the file ELI1537.ali  (no gaps) :

>P1;ELI1537
sequence:ELI1537:::::::0.00:0.00
MAGPSLGEWKAKAQHFAYDGLQIAFWTGGKPDARPLLLVHGYPTASWDWHRVWETLGSKY
HLVAPDMIGFGLSDKPRSGYSIHRQADMHVALLDHLGIGAFDALVHDYGVSVGQELLARR
AERSAAQGLGQAQDTTNGGIFPDQHRPRPIQKLGTSPLGFLVGLLTNREKFGRSFSEVFGP
DTQPGAQELDEFWDLVSHNGGNRIMHKLLHYIADRKEHAERWFDALRIAQGDIGLINGAL
DPVSGRHAYEAWRERLPDARHHLIPTVGHYPQVEDPQTVSRVTLDWLAR*
The file build_profile.py is:
from modeller import *
log.verbose()
env = environ()
sdb = sequence_db(env)
sdb.read(seq_database_file='pdb_95.pir', seq_database_format='PIR',
         chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)
sdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
          chains_list='ALL')
sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
         chains_list='ALL')
aln = alignment(env)
aln.append(file='ELI1537.ali', alignment_format='PIR', align_codes='ALL')
prf = aln.to_profile()
prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat',
          gap_penalties_1d=(-500, -50), n_prof_iterations=1,
          check_profile=False, max_aln_evalue=0.01)
prf.write(file='build_profile.prf')
aln = prf.to_alignment()
aln.write(file='build_profile.ali', alignment_format='PIR')
I also copy the file pdb_95.pir to the current directory. I don't
understand why there're errors that is:
Traceback (most recent call last):
  File "build_profile.py", line 23, in ?
    aln.append(file='ELI1537.ali', alignment_format='PIR',
align_codes='ALL')  File
"/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 36, in
append
    return self.__int_append('alignment.append', io, libs, vars)
  File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 68,
in __int_append
    libs=libs.modpt, **vars)
  File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 33, in
read_alignment
    return _modeller.read_alignment(aln, io, libs, *args)
_modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was
not found in the alignment file; ALIGN_CODES(       1) =  ALL
Please help me to solve this error, I try to find answers in modeller
forum but it's no use. Thank you very much!
Best regards,
NGODUCTRI