On 1/13/14 9:32 AM, ms wrote: > I am trying to perform loop optimization on a protein structure which > contains a non-standard ligand. ... > transfe_404W> At least one template is aligned with model residue 309:B > but no coordinates could be transferred. This usually > occurs when your input files do not use the official > PDBv3 atom names. Please check your templates.
I'd be interested to see why this is happening. The most likely explanation is that your non-standard residue has the same name as one Modeller knows about, but contains a different set of atoms. But loop modeling should take your input, regardless of what Modeller thinks it knows. If you can also send me your input PDB, I'll take a look.
Ben Webb, Modeller Caretaker