[MMTK] Problems loading certain PDB files

khinsen@cea.fr khinsen at cea.fr
Mon Jan 23 15:43:13 CET 2006


On Jan 20, 2006, at 17:41, Peter wrote:

> I am using MMTK-2.5.13 under Python 2.3.3 on Windows XP.  I don't know
> what version of Scientific python I have - does it matter?

No - unidentified atoms have always raised and will always raise  
exceptions.

> My only guess for what 'AE1', 'AE2', 'AD1' and 'AD2' mean is based on
> Appendix 3 of the format definition: "Atoms for which some ambiguity
> exists in the crystallographic results are designated A".  Are this
> probably Hydrogrens?

I don't think so, for physical reasons: hydrogens are very much  
smaller than anything else in an electronic density map. With  
insufficient resolution, a hydrogen atom becomes undetectable but I  
wouldn't expect it to be confused with some heavier atom.

My first reaction to seeing such atom names would be to consult the  
comments in the file and then the corresponding publication.

Konrad.
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