Re: [modeller_usage] Loop optimization starting from a structure with ligand

[Modeller Caretaker <>]

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
--
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