Hi All,
I found that model.write_data() ignores mercury ions (HG) when writing .ngh files (e.g. 1AVN.pdb, 1OKM.pdb). It also ignores UNX (UNKNOWN ATOM OR ION), in which case I understand.
I checked whether mercury ions are ignored because it's not in modeller-9v8/modlib/restyp.lib, but I don't think so because LI1 (in 2I21.pdb) and DOD (in 1CQ2.pdb) are not ignored.
Is there a reason why mercury ions should be ignored? Are there any other specific records that model.write_data() will ignore?
Thank you!
- Yingjie
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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Modeller Caretaker -
Yingjie Lin