Re: [modeller_usage] mercury ions ignored by model.write_data()

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 01/26/2011 03:09 PM, Yingjie Lin wrote:
> I found that model.write_data() ignores mercury ions (HG) when writing
> .ngh files (e.g. 1AVN.pdb, 1OKM.pdb).

Actually, it's not write_data(), but it's the reading in of the initial 
PDB file. Modeller thinks HG is a hydrogen atom and by default it 
ignores those (until comparatively recently there was no way to tell 
whether HG was hydrogen or mercury, since PDB files didn't identify the 
element). If you set env.io.hydrogen = True, it should work. I will fix 
this for the next Modeller release.

write_data() itself should handle all residue types, whether or not they 
are defined in restyp.lib.

	Ben Webb, Modeller Caretaker
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