[MMTK] Problems loading certain PDB files

khinsen@cea.fr khinsen at cea.fr
Mon Jan 23 12:10:50 CET 2006


On Jan 22, 2006, at 13:59, Peter wrote:

> It turns out PDB file 1BTY is littered with multiply defined atoms  
> (including hydrogens).  I would guess MMTK cope with these, but  
> when asked to delete a hydrogen twice, on the second attempt the  
> dictionary element has already been removed.

MMTK does cope with alternate atom definitions by reading only one of  
the alternatives. You can specify the one you want using an optional  
argument to PDBConfiguration, the default being A.

What is particular about 1BTY is that some residues have atoms with  
alternate labels but also a version without an alternate label. I  
have never seen that before, nor do I know how this is supposed to be  
interpreted. It is those atoms that cause the crashes because both  
the unlabelled version and the version labelled A are taken into  
account.

In my opinion, the PDB format definition does not permit unlabelled  
alternate positions. Here is the relevant paragraph:

	If an atom is provided in more than one position, then a non-blank  
alternate
	location indicator must be used as the alternate location indicator  
for each
	of the positions. Within a residue all atoms that are associated  
with each
	other in a given conformation are assigned the same alternate  
position indicator.

I cannot propose any solution at the moment, other than modifying the  
PDB file by hand.

Konrad.
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Konrad Hinsen
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