Fwd: modeling with multiple sequence alignment.
---------- 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. > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > >
Your script looks like OK to me...
It looks like an error regarding system permissions.
Try to copy the folder in a common user area and run it again.
Maybe Ben Webb has another suggestion...
good lucky
Flavio
--- On Mon, 12/10/12, Krupal Jethava krupal.jethava@gmail.com wrote:
From: Krupal Jethava krupal.jethava@gmail.com Subject: [modeller_usage] Fwd: modeling with multiple sequence alignment. To: modeller_usage@salilab.org Date: Monday, December 10, 2012, 12:32 PM
---------- 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 templates2) 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 formsdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY', chains_list='ALL')
#-- Now, read in the binary databasesdb.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 formatprf = aln.to_profile() #-- Scan sequence database to pick up homologous sequencesprf.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 formatprf.write(file='build_profile.prf', profile_format='TEXT')
#-- Convert the profile back to alignment formataln = prf.to_alignment() #-- Write out the alignment filealn.write(file='build_profile.ali', alignment_format='PIR')
There is errorcannot 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.
> _______________________________________________
> modeller_usage mailing list
> modeller_usage@salilab.org
> https://salilab.org/mailman/listinfo/modeller_usage
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