Do you have to use the modeller alignment script? I have been using ebi
software to create a .pir file.
No, you do not need to use Modeller to make your alignment file.
However, since there are no standard one-letter codes for ligands, you
will likely have to edit your original alignment in a text editor to put
in the ligands.
After reading the modeller files and tutorials i am still at a loss as to
how to use these 'blk' characters. I am trying to get a molecule of fad
that is present in my template into my model.
Please go through the advanced tutorial, and if you have a specific
question, ask it. You could also post your input files. Otherwise, I can
only give reiterate what's in the documentation, since I don't know what
your stumbling block is.