[phenixbb] Dummy atoms

Pavel Afonine pafonine at lbl.gov
Wed Jul 28 08:53:49 PDT 2010

  Hi Frank,

thanks a lot for your feedback - as always very useful and critical 
which is great!

> the 2nd-last one of the validation pack, where you recommend against 
> the use of UNK atoms, but don't say why:
> <snip>
> Some programs and people tend to interpret unknown density using "dummy
> atoms". In PDB files it typically looks like this:
> ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X
> ATOM 11 O UNK 2 6.994 -12.600 10.740 1.00 7.16 X
> ATOM 12 O UNK 2 6.028 -13.737 10.607 1.00 6.58 X
> ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28
> ATOM 14 DUM UNK 2 5.099 -13.727 11.792 1.00 7.15
> - *Do not deposit this in PDB*, especially if chemical element type is 
> undefined
> (rightmost column)
> </snip>

Sorry for not saying "why". If it ever happens for me to show these 
slides again in whatever School I promise to improve the slides to be as 
clear as possible.

The problems with records like:

ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X
ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 X


- the chemical element type (column 77-78 ?) (that one that use in Fcalc 
calculation and also may provide the charge) is undefined (simply blank 
or "X"), so there is no way to include these dummy atoms into structure 
factor calculations;

- even if you have "O" like in the first example this often contradicts 
with "X" in rightmost column, so you have to use guesswork, which is not 
good for interpreting well defined formatted data files. Plus, of 
course, not way to tell the charge;

- even if you have "O" like in the second example the element type in 
rightmost column is missing. Therefore it is a weak information to take: 
we cannot reliably extract scattering type from atom label - classical 
example CA (Calcium) and CA (C-alpha);

- of course, we can make the program simply ignore these atoms (hm... 
sounds like a bad practice: don't read it if you can't read it - this 
way we may end up being ignorant -:) ). But are we sure that the 
original program that put these dummies was also not using them in Fcalc 
calculation? Or may be it was using some default scattering factor for 
them? Which one: H or O or N (N better approximates than O)?

- furthermore, since we are lacking such a fundamental property of these 
dummy atoms as scattering type, it it laughable to assign some B-factors 
to these atoms! Look through PDB: you will find a some smart looking 
B-factors, such as 8.06 A**2 for an non-existing element X -:)

In summary:

- do not put there anything hoping that future generation smarter 
software will find out what it is;
- if you want to put something there (which has valid reasons actually - 
this will improve the overall map quality which is good - then please 
properly define it).

All the best!

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