•·.·´¯`·.·• Iƒƒ¥ •·.·´¯`·.·• wrote:
> I m having problems in multiple alignment through modeller. I have
> protien sequence in fasta format and am doing alignment from the
> start. For this purpose i have used model-full.py file but it gives
> the following error. I am unable to understand the error. What I m
> doing wrong?
Please look at the examples in the Modeller manual. Your alignment file
is not valid PIR format (it is not FASTA format either). What you
probably want is actually something like the following:
>P1;AIRE
sequence:AIRE::::::::
MATDAALRRLLRLHRTEIAVAVDSAFPLLHALADHDVVPEDKFQETLHLKEKEGCPQAFHALLSWLLTQDSTAILDFWRVLFKDYNLERYGRLQPILDSFPKDVDLSQPRKGRKPPAVPKALVPPPRLPTKRKASEEARAAAPAALTPRGTASPGSQLKAKPPKKPESSAEQQRLPLGNGIQTMSASVQRAVAMSSGDVPGARGAVEGILIQQVFESGGSKKCIQVGGEFYTPSKFEDSGSGKNKARSSSGPKPLVRAKGAQGAAPGGGEARLGQQGSVPAPLALPSDPQLHQKNEDECAVCRDGGELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQATVQEVQPRAEEPRPQEPPVETPLPPGLRSAGEEVRGPPGEPLAGMDTTLVYKHLPAPPSAAPLPGLDSSALHPLLCVGPEGQQNLAPGARCGVCGDGTDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTPAPVEGVLAPSPARLAPGPAKDDTASHEPALHRDDLESLLSEHTFDGILQWAIQSMARPAAPFPS*
>P1;2AZW
structureX:2AZW:FIRST:@:LAST:@::::
*
>P1;1XWH
structureX:1XWH:FIRST:@:LAST:@::::
*
>P1;1H5P
structureX:1H5P:FIRST:@:LAST:@::::
*
>P1;1M9D
structureX:1M9D:FIRST:@:LAST:@::::
*
i.e. the 'sequence:AIRE' line must have 10 colon-separated fields, and
you need to specify the residue ranges to read from each PDB file (here
I asked Modeller to read everything from the first chain). I don't know
exactly what is wrong with the template PDB files you used, because you
didn't attach them, but if you use PDB files from PDB itself, you would
get a message like the following with your original alignment:
get_seq_385E> No primary sequence was read from PDB file " ./1H5P.pdb",
since the starting residue number " "
and/or chain id " " given in the alignment file header
were not found in the PDB.
which should be pretty clear in pointing to a mismatch between the
alignment file header and your PDB file as the problem.
I recommend that you don't try to build your homology models this way,
however. They will be of very low quality. Your templates are not very
similar to each other, so Modeller will have a hard job aligning them.
Even if you remove some of the templates, I don't recommend you use this
automatic method to align them, since the sequence identity is low.
Instead, you should use a good sequence-structure alignment method to
determine your initial alignment.
Ben Webb, Modeller Caretaker
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