Re: [modeller_usage] Alignment errors model not running

[Thomas Juettemann <>]

Also make sure that you use the sequence derived from the ATOM records
rather then from the SEQRES records. Dunbracks S2C is an excellent
resource for that:

http://dunbrack.fccc.edu/Guoli/s2c/index.php

If MODELLER still crashes have a look at the start and end of each
chain. It maybe that on residue only has coordinates for 1 N. Delete
that ATOM record in that case.

Cheers,
Thomas

On Tue, Apr 27, 2010 at 10:17, Thomas Juettemann <> wrote:
> Likely that you did not define the range in the comment line, more
> detailed information about the alignment format can be found here:
> http://salilab.org/modeller/manual/node445.html#alignmentformat
>
> This might might work:
>
> P1;1ATG
> structureX:1ATG:FIRST:@ END::::::
> ELKVVTATNFLGTLEQLAGQFAKQTGHAVVISSGSSGPVYAQIVNGAPYNVFFSADEKSPEKLDNQGFALPGSRFTYAIG
> KLVLWSAKPGLVDNQGKVLAGNGWRHIAISNPQIAPYGLAGTQVLTHLGLLDKLTAQERIVEANSVGQAHSQTASGAADL
> GFVALAQIIQAAAKIPGSHWFPPANYYEPIVQQAVITKSTAEKANAEQFMSWMKGPKAVAIIKAAGYVLPQ
>
> Cheers,
> Thomas
>
> On Tue, Apr 27, 2010 at 02:21, Daniel Fernandez <> wrote:
>> sorry i forgot to attach the target sequence... it's the fasta sequence of
>> the 1ATG protein...
>>
>> On Mon, Apr 26, 2010 at 8:19 PM, Daniel Fernandez <> wrote:
>>>
>>> Hi,
>>>
>>> Please help me with this error.  I have been more than a week trying to
>>> solve this issue and I still can't solve it.
>>>
>>> Let me explain my approach to use modeller.
>>>
>>> First I search for templates against the pdb database
>>> I select as templates the one with low e-value and reasonable similarity
>>> percentage
>>> I use clustalW (or TCoffee) to align the target and the selected
>>> templates.
>>> I use modeller to model the target based on the TCoffee alignment file and
>>> the PDB files.
>>>
>>> I do the whole pipeline but modeller works for some sequences but for most
>>> of them it gives me the following error and at this point I am clueless on
>>> how to solve it.  Here I attach my input files to modeller in case someone
>>> wants to take a look at them and help me solve this issue.
>>>
>>> INPUT:  finalseq.pir (as in modeller format, i tried all different formats
>>> here, I attach my last approach that was to only save PDB files with the
>>> data from a specific chain...)
>>>              template PDB files (the PDB files with the actual chain)
>>>              target.fasta
>>>
>>> OUTPUT: error:
>>> get_ran_648E> Alignment sequence not found in PDB file:        3
>>> 2H5Y_A.pdb
>>>               (You didn't specify the starting and ending residue numbers
>>> and
>>>               chain IDs in the alignment, so Modeller tried to guess these
>>> from
>>>               the PDB file.)
>>>               Suggestion: put in the residue numbers and chain IDs (see
>>> the
>>>               manual) and run again for more detailed diagnostics.
>>>               You could also try running with allow_alternates=True to
>>> accept
>>>               alternate one-letter code matches (e.g. B to N, Z to Q).
>>> Traceback (most recent call last):
>>>   File "testclean.py", line 18, in <module>
>>>     a.make()          # do the homollogy modelling
>>>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line
>>> 98, in make
>>>     self.homcsr(exit_stage)
>>>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line
>>> 411, in homcsr
>>>     aln = self.read_alignment()
>>>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line
>>> 401, in read_alignment
>>>     aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])
>>>   File "/n/sw/modeller-9v7/modlib/modeller/alignment.py", line 79, in
>>> append
>>>     allow_alternates)
>>> _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not
>>> found in PDB file:        3  2H5Y_A.pdb (You didn't specify the starting and
>>> ending residue numbers and chain IDs in the alignment, so Modeller tried to
>>> guess these from the PDB file.) Suggestion: put in the residue numbers and
>>> chain IDs (see the manual) and run again for more detailed diagnostics. You
>>> could also try running with allow_alternates=True to accept alternate
>>> one-letter code matches (e.g. B to N, Z to Q).
>>>
>>> I am completely clueless on where to look the starting and ending residue
>>> numbers and chain IDs in the alignment, clustalW does not give me that
>>> information at all so not sure where to look that info and if possible with
>>> the approach I am using...
>>>
>>> Thanks,
>>>
>>> Daniel F.
>>
>>
>>
>> --
>> Daniel F.
>>
>> Department of Statistics, Harvard University
>> 1 Oxford Street, Cambridge, MA 02138
>>
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