[modeller_usage] Error when reading the alignment PIR file.

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.

--
Daniel F.

Department of Statistics, Harvard University
1 Oxford Street, Cambridge, MA 02138