[modeller_usage] Fwd: modeling with multiple sequence alignment.

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

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 <" target="_blank">> 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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