Hello sir,

I have executed the following code.

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='TvLDH.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')

the following messages are displayed.

1)file build_profile.py line 6 in? seq_database_format='PIR', chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)

2) file c:\programfiles\modeller8v2\modlib\modeller\util\top.py line 29 in read. libs=libs.modpt , **vars

3)file c:\programfiles\modeller8v2\modlib\modeller\util\top.py line 353 line in read_sequence_db return modeller.read_sequence_db(sdb,libs,*args)

4) IO error openf 670E)cannot open file pdb_95.PIR no such file or directory

1,2,3----are these errors or warnings.

please kindly let me know the changes i have to make.

Regards suneetha.

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