Re: [modeller_usage] construct a model with a ligand

On 10/2/13 1:04 AM, fantasticqhl wrote: > >P1;1ze9A > structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00 > DAEFRHDSGYEVHHQK-* ... > Right now, I guess that the error is coming from the alignment, but I > did not find how the alignment was done in the tutorial.

You need to modify the alignment by hand (in a text editor). You'll need to add a '.' to the structure corresponding to the position of the Zn residue in the PDB sequence (most likely at the end), and align it with the Zn in your model. And you'll need to change the "+16" in the header (instructing Modeller to read 16 residues from the PDB file) to "+17".

Ben Webb, Modeller Caretaker