I am trying to search for the best template for my target molecule, and therefore I created a file in PIR format with my sequences and then
I ran build_profile.py. I got the following error in my log file:
MODELLER 9.10, 2011/09/28, r8346
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2011 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux pan 3.0.0-12-generic x86_64
Date and time of compilation : 2011/09/28 17:58:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2012/02/29 16:37:57
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v10}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v10}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085
openf___224_> Open ${MODINSTALL9v10}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 3.131
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL9v10}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140
openf___224_> Open ${MODINSTALL9v10}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v10}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v10}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v10}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v10}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v10}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v10}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
openf___224_> Open pdb.pir
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3293057 3215.876 3.141
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3294891 3217.667 3.142
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3296341 3219.083 3.144
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3299241 3221.915 3.146
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305041 3227.579 3.152
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3310040 3232.461 3.157
SEQ_DATABASE_FILE : pdb.pir
SEQ_DATABASE_FORMAT : PIR
CHAINS_LIST : ALL
CLEAN_SEQUENCES : T
MINMAX_DB_SEQ_LEN : 30 4000
Number of sequences : 4
Number of residues : 1060
Length of longest sequence: 271
SEQ_DATABASE_FILE : pdb_3.bin
SEQ_DATABASE_FORMAT : BINARY
SEARCH_CHAINS_LIST : ALL
Number of sequences : 4
Number of residues : 1060
Length of longest sequence: 271
SEQ_DATABASE_FILE : pdb_3.bin
SEQ_DATABASE_FORMAT : BINARY
CHAINS_LIST : ALL
CLEAN_SEQUENCES : T
MINMAX_DB_SEQ_LEN : 0 999999
Number of sequences : 4
Number of residues : 1060
Length of longest sequence: 271
openf___224_> Open chst11.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3300046 3222.701 3.147
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3301496 3224.117 3.149
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3304396 3226.949 3.151
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3310196 3232.613 3.157
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3311600 3233.984 3.158
Read the alignment from file : chst11.ali
Total number of alignment positions: 352
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 chst11 352 1 chst11
Dynamically allocated memory at amaxprofile [B,KiB,MiB]: 3313325 3235.669 3.160
openf___224_> Open ${LIB}/blosum62.sim.mat
rdrrwgh_268_> Number of residue types: 21
profile_iteration_> processing sequence: 1 352 1 0.0100000 0.0100000 0.0100000 1
regress_657E> Not enough bins in histogram - cannot calculate statistics, nbins: 1
from modeller import *
log.verbose()
env = environ()
#-- Prepare the input files
#-- Read in the sequence database
sdb = sequence_db(env)
sdb.read(seq_database_file='pdb.pir', seq_database_format='PIR',
chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)
#-- Write the sequence database in binary form
sdb.write(seq_database_file='pdb_3.bin', seq_database_format='BINARY',
chains_list='ALL')
#-- Now, read in the binary database
sdb.read(seq_database_file='pdb_3.bin', seq_database_format='BINARY',
chains_list='ALL')
#-- Read in the target sequence/alignment
aln = alignment(env)
aln.append(file='chst11.ali', alignment_format='PIR', align_codes='ALL')
#-- Convert the input sequence/alignment into
# profile format
prf = aln.to_profile()
#-- Scan sequence database to pick up homologous sequences
prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat',
gap_penalties_1d=(-500, -50), n_prof_iterations=10,
check_profile=True, 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')
If anyone could help me with this I would be grateful.