When i run this program showing an error
from modeller import * log.verbose() env = environ()
#-- Prepare the input files
#-- Read in the sequence database sdb = sequence_db(env) sdb.read(seq_database_file='pdb95.fsa', seq_database_format='FASTA', chains_list='ALL', minmax_db_seq_len=(1, 40000), clean_sequences=True)
#-- Write the sequence database in binary form sdb.write(seq_database_file='pdb95.bin', seq_database_format='BINARY', chains_list='ALL')
#-- Now, read in the binary database sdb.read(seq_database_file='pdb95.bin', seq_database_format='BINARY', chains_list='ALL')
#-- Read in the target sequence/alignment aln = alignment(env) aln.append(file='toxin.ali', alignment_format='PIR', align_codes='ALL')
#-- Convert the input sequence/alignment into # profile format prf = aln.to_profile()
#-- Scan sequence database to pick up homologous sequences prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat', gap_penalties_1d=(-500, -50), n_prof_iterations=5, check_profile=False, max_aln_evalue=0.01, gaps_in_target=False)
#-- Write out the profile prf.write(file='buildprofile.prf', profile_format='TEXT')
#-- Convert the profile back to alignment format aln = prf.to_alignment()
#-- Write out the alignment file aln.write(file='buildprofile.ali', alignment_format='PIR')
could not open the file pdb_95.fsa
where i get this file??
On 03/07/2011 11:21 AM, Bishwajit Das wrote: > When i run this program showing an error ... > could not open the file pdb_95.fsa
Since the PDB is continually being added to, we do not distribute this file with Modeller.
> where i get this file??
You can make it yourself from PDB, or you can download it (but in PIR format, not FASTA) from http://salilab.org/modeller/supplemental.html
Ben Webb, Modeller Caretaker
participants (2)
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Bishwajit Das
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Modeller Caretaker