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*:*endresidue :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,