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