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@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. >