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 <dfernan(a)gmail.com> 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.
>
> 1. First I search for templates against the pdb database
> 2. I select as templates the one with low e-value and reasonable
> similarity percentage
> 3. I use clustalW (or TCoffee) to align the target and the selected
> templates.
> 4. 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
