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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: [mailto:]
On Behalf Of Austin Baker 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') Everything is Experimental |