Charlie Allerston wrote: > 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.
Ben Webb, Modeller Caretaker