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