[phenixbb] phenix.refine change: support for residues onsymmetryelements

Pavel Afonine PAfonine at lbl.gov
Sun Dec 27 14:19:47 PST 2009

Hi Maia,

> when I submitted a pdb with some waters on a twofold sym. axis with 
> occupancies =1, the PDB wanted occupancies 0.5.
> They do not want to take into account your "taken into account 
> internally".

Hopefully, time will heal it -:)

More seriously (I wrote it somewhere for someone, even not once):

The maximal multiplicity of a special position in proteins is 24 (or so, 
correct me if I'm wrong, please), and the precision of the occupancy 
factor field in PDB file is only two digits. Let’s imagine a relatively 
small structure at high resolution that contains a handful amount of 
heavy atoms all located at special positions with the multiplicity 24. 
Now, the occupancies of these heavy atoms in a PDB file all have to be 
set to 1./24 ~ 0.04 and not to 0.042. Depending on the number of 
electrons in a heavy atom, the number of heavy atoms, multiplicity of 
special position and overall structure size, one can easily imagine a 
situation when this kind of rounding error may become very significant. 
Therefore, I think, it is a bad idea to rely on the file format in this 
case, and is much better to do this trivial operation internally without 
any unnecessary loss of accuracy. Plus, it all happens seamlessly for 
the end-user, which is another step towards the automation.


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