On Mon, Apr 12, 2010 at 08:08, Daniel Fernandez <
dfernan AT gmail.com> 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
>