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

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 :

>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*

# 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