[modeller_usage] Sequence Mismatch Errors

22 Jun 2012


      All,
I am trying to run a 2d alignment and keep getting a number of errors that I have been unable to rectify. In addition to the error message presented below I've also been getting one that says "Alignment sequence not found in the pdb file".
Much appreciated in advance
Austin
ERROR MESSAGE:
    Traceback (most recent call last):
  File "align2d_HDAC9a_Cat.py", line 21, in <module>
    align_block=aln_block)
  File "/Library/modeller-9.10/modlib/modeller/alignment.py", line 299, in align2d
    smooth_prof_weight, weights_type)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and  pdb :
ALIGNMENT FILE:
>P1;HDAC9a_Cat
sequence:HDAC9a_Cat:1:A:251:A:::::
PGSATGIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLV
HSEHHSLLYGTNPLDGQKLDPRILLGDDSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELAS
KVASGELKNGFAVVRPPGHHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYA
DPSILYISLHRYDEGNFFPGSGAPNEVRFISLEPHFYLYLSGNCIA*
>P1;2vqj
StructureX:2vqj.pdb:6:A:236:A:::0.00: 0.00
GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTV
HSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFK
VATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSD
PSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAP
DVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLG
NELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT*
SCRIPTS
# Demonstrating ALIGN2D, aligning with variable gap penalty
from modeller import *
log.verbose()
env = environ()
env.libs.topology.read('$(LIB)/top_heav.lib')
env.io.atom_files_directory = ['./atom_files']
# Read aligned structure(s):
aln = alignment(env)
aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')
aln_block = len(aln)
# Read aligned sequence(s):
aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')
# Structure sensitive variable gap penalty sequence-sequence alignment:
aln.align2d(overhang=0, gap_penalties_1d=(-100, 0),
            gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.),
            align_block=aln_block)
aln.write(file='align2d.ali', alignment_format='PIR')
aln.write(file='align2d.pap', alignment_format='PAP',
          alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \
                             'ACCESSIBILITY CONSERVATION')
aln.check()
# Color the first template structure according to gaps in alignment:
aln = alignment(env)
aln.append(file='align2d.ali', align_codes=('HDAC9a_Cat', '2vqj'),
           alignment_format='PIR', remove_gaps=True)
mdl = model(env)
mdl.read(file=aln['HDAC9a_Cat'].atom_file,
         model_segment=aln['HDAC9a_Cat'].range)
mdl.color(aln=aln)
mdl.write(file='HDAC9a_Cat.aln.pdb')
# Color the first template structure according to secondary structure:
mdl.write_data(file='HDAC9a_Cat', output='SSM')
mdl.write(file='HDAC9A_Cat.ssm.pdb')
# Superpose the target structure onto the first template:
mdl2 = model(env)
mdl2.read(file=aln['2vqj'].atom_file,
          model_segment=aln['2vqj'].range)
sel = selection(mdl).only_atom_types('CA')
sel.superpose(mdl2, aln)
mdl2.write(file='2vqj.fit.pdb')
Austin Baker
asb93@pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh
Everything is Experimental