[Chimera-users] save pdb in the same order

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 13 11:11:43 PDT 2007

Hi Laura,
	Chimera's PDB support was written with macromolecules in mind and  
adheres as closely as possible to the PDB standard.  This means that  
it outputs amino and nucleic acid atoms within a residue in the same  
order that the PDB uses, regardless of original input order.  Not  
much thought was given to the order of "other" residue atoms, and  
they basically come out in random order -- which is obviously bad in  
your case.
	I'm going to open a bug report on this, with you on the recipient so  
that you will know when the behavior is fixed.  Until then, the only  
way to preserve ordering is to output in some other format, e.g.  
Mol2, which may or may not be acceptable for what you're doing.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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