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
On 06/22/2012 12:45 PM, Austin Baker wrote: > I am trying to run a 2d alignment and keep getting a number of errors > that I have been unable to rectify.
When you get a SequenceMismatchError, Modeller also reports in the log file the sequence you gave in the alignment file and the sequence it found in the PDB, so you can see where the mismatch occurred. Look in the log file and change either your alignment or the PDB file so the sequences match.
> In addition to the error message > presented below I've also been getting one that says "Alignment sequence > not found in the pdb file".
The actual error message with context would be useful here.
Ben Webb, Modeller Caretaker
Hi there,
Looking at your alignment, firstly, the sequence of the pdb file is shorter than the sequence listed (some residues may be disordered. Secondly the numbering StructureX:2vqj.pdb:6:A:236:A - the pdb file (similar to your sequence actually goes to ~residue 406. If you are only after a domain then that is reasonable but I would delete the unwanted residues (sequence and actual pdb file)
Hope this helps
Joel
From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Austin Baker Sent: Saturday, 23 June 2012 7:45 a.m. To: modeller_usage@salilab.org Subject: [modeller_usage] Sequence Mismatch Errors
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.edumailto:asb93@pitt.edu Graduate Student Department of Chemistry University of Pittsburgh
Everything is Experimental
participants (3)
-
Austin Baker -
Joel Tyndall -
Modeller Caretaker