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.edu

Graduate Student

Department of Chemistry

University of Pittsburgh

Everything is Experimental