---------- Forwarded message ----------
From: Krupal Jethava <krupal.jethava@gmail.com>
Date: Mon, Dec 10, 2012 at 5:12 PM
Subject: Re: [modeller_usage] modeling with multiple sequence alignment.
To: Rienk Doetjes <rienk@stereodax.com>


I have these files.
1) alignment2.ali file for alignment between target (qseq) and templates (tseq1, tseq2).
2) pdb files of templates
2) script.py

I tried this script as first step.

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='pdb_95.pir', seq_database_format='PIR',
         chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)

#-- Write the sequence database in binary form
sdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
          chains_list='ALL')

#-- Now, read in the binary database
sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
         chains_list='ALL')

#-- Read in the target sequence/alignment
aln = alignment(env)
aln.append(file='alignment2.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=1,
          check_profile=False, max_aln_evalue=0.01)

#-- Write out the profile in text format
prf.write(file='build_profile.prf', profile_format='TEXT')

#-- Convert the profile back to alignment format
aln = prf.to_alignment()

#-- Write out the alignment file
aln.write(file='build_profile.ali', alignment_format='PIR')

There is error
cannot open logfile script.log: permission denied.




On Mon, Dec 10, 2012 at 5:04 PM, Rienk Doetjes <rienk@stereodax.com> wrote:
Could you provide more information? Could you post your script, the error you receive, etc?

On 10 Dec 2012, at 11:26, Krupal Jethava wrote:

> Dear Sir,
>    I am trying to use modeller for multiple sequence alignment but I got error while running script for DOPE score. will you guide from the beginning. how to make input file and which script should I use for that. Thanks.
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