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Hello Krish--
>
> I am trying to use the 'refine.py' to refine the structures generated under
> cyana 2.1. Unfortunately, I get the following error.
> (protocol.loadPDB("test_i.pdb"
> )). I tried to save the file in various formats (IUPAC/xplor or pdb) using
> the 'translate' option with cyana, same error!
>
loadPDB works with files in IUPAC naming. The question is: what do these
atoms correspond to?
>
> PDBTool:read: atom not found in structure: A SER 1 HB3(name converted from
> 3HB)
> PDBTool:read: atom not found in structure: A SER 1 HB'(name converted from
> HB*)
> PDBTool:read: atom not found in structure: A LYS 2 HB3(name converted from
> 3HB)
If you send me a complete PDB file I *might* be able to expand loadPDB's
heuristics for atom matching so that these files load.
best regards--
Charles
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