Re: [modeller_usage] Alignment errors model not running

[Thomas Juettemann <>]

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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