Re: [modeller_usage] Error when reading the alignment PIR file.

[Thomas Juettemann <>]

You need to specify which part of the sequence of your template you
are using. Not specifying it causes the error message "Alignment
sequence not found in PDB file...".
You can find more information about the alignment format here:
http://salilab.org/modeller/manual/node445.html#alignmentformat
Also, your template seems to be a NMR structure, you need to replace
the structureX with NMR.

Try using these sequences in your alignment file:

P1;1aho
sequence:1aho:FIRST:@ END::::::
VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK
LPDHVRTKGPGRCH--*

P1;2kbhA
NMR:2kbh.pdb:FIRST:@ END::::::
VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK
LPDDARIMKPGRCNGG*



On Mon, Apr 12, 2010 at 08:08, Daniel Fernandez <> wrote:
> Hi,
> Please help me if possible, I have been stuck few days by now :-(
> I am trying a very basic approach to use modeller, but in this case I am
> using my own global alignment from clustalW.  I am trying a very basic
> protein, target: 1aho, and only one template 2kbh_A
> ClustalW outputs the alignment in PIR format
> (http://www.bioinformatics.nl/tools/crab_pir.html) but is a different PIR
> format than the one required by modeller.  Actually the main difference is
> that clustalW does not provide the start residue:start chain code:end
> residue:end chain code: parts.
> I do not know how to get that information and modeller apparently does not
> know either. Here I copy and paste the clustalW PIR format, the PIR modeller
> format and the errors I get from the model_simple.log.
> CLUSTALW PIR format - sequencealn.pir
>>P1;1AHO_A|PDBID|CHAIN|SEQUENCE
> VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK
> LPDHVRTKGPGRCH--
> *
>>P1;2KBH_A|PDBID|CHAIN|SEQUENCE
> VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK
> LPDDARIMKPGRCNGG
> *
> MODELLER INPUT (does not work, not sure why)
>>P1;1aho
> sequence:1aho:     : :     : ::: 0.00: 0.0
> VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYK
> LPDHVRTKGPGRCH--*
>>P1;2kbhA
> structureX:2kbh.pdb:     : :     : ::: 0.00: 0.0
> VKDGYIADDRNCPYFCGRNAYCDGECKKNRAESGYCQWASKYGNACWCYK
> LPDDARIMKPGRCNGG*
> ERROR MODELLER GIVES ME:
> get_ran_648E> Alignment sequence not found in PDB file:        1  2kbh.pdb
>               (You didn't specify the starting and ending residue numbers
> and
>               chain IDs in the alignment, so Modeller tried to guess these
> fr
>               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 "hoModeller-clustalaln.py", line 14, in <module>
>     a.make()          # do the homollogy modelling
>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line 98,
>     self.homcsr(exit_stage)
>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line
> 411,
>     aln = self.read_alignment()
>   File "/n/sw/modeller-9v7/modlib/modeller/automodel/automodel.py", line
> 401,
>     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
> i
> I am aware that the error advice me to put the start and ending residues
> numbers but I am still not sure how to solve the issue.
> Any help will be strongly appreciated, I need to use modeller as soon as
> possible to do some progress in my research.
> Best,
> --
> Daniel F.
>
> Department of Statistics, Harvard University
> 1 Oxford Street, Cambridge, MA 02138
>
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