•·.·´¯`·.·• 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