BIN ZHANG wrote: > I was trying to add missing residues in pdb file according to the page: > > http://salilab.org/modeller/wiki/Missing%20residues > > But, one thing I don't understand is how can I get the "alignment.ali" file?

You have to create it manually. You can add the missing residues by reading the REMARK lines in the PDB to figure out which ones are missing, and then perhaps the SEQRES lines to figure out what the residue types are.

> Aslo, it seems to me the command complete_pdb() can also do the job? > http://salilab.org/modeller/manual/node403.html > Is this true? If so, what's the difference between these 2?

No - complete_pdb does not add missing residues. It adds any missing *atoms* for any residue - for example, if your input PDB contains only CA coordinates, it will add (using internal coordinates) the rest of the backbone and sidechain. But it won't add any residues that aren't in the PDB in the first place.

Ben Webb, Modeller Caretaker