Also make sure that you use the sequence derived from the ATOM records rather then from the SEQRES records. Dunbracks S2C is an excellent resource for that:

http://dunbrack.fccc.edu/Guoli/s2c/index.php

If MODELLER still crashes have a look at the start and end of each chain. It maybe that on residue only has coordinates for 1 N. Delete that ATOM record in that case.

Cheers, Thomas

On Tue, Apr 27, 2010 at 10:17, Thomas Juettemann juettemann@gmail.com wrote: > 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 >> >> >