[modeller_usage] errors after running the program

[gadde suneetha <>]

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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