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 dfernan@gmail.com 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 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. >> >> 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 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >