On 3/19/24 8:38 AM, hmad3--- via modeller_usage wrote: > What if I am modelling with ligands? Would the following be right? > temp1 AAAA./AAAA/BBBB./BBBB/BBBB* > temp2 aaaa-/----/----/----/----* > temp3 ----/-----/bbbb-/----/----* > model aaaa./aaaa/bbbb./bbbb/bbbb*
Yes. Normally I would align the chain breaks with each other to make it more clear to a human reader, but Modeller doesn't distinguish a chain break from a gap in a template.
> (The .pdb files for temp2 and temp3 have no ligands. Should the > ligand be indicated? If so, with a "-" or "."?)
The sequence for a template must match what's in the PDB file. So if there is no ligand, there should be no ".". Normally you would put a gap here so that the target does not align with anything else in that template at that position. (Generally it only makes sense for a target ligand to align with a single template ligand.)
Ben Webb, Modeller Caretaker