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Hi Frank,<br>
<br>
thanks a lot for your feedback - as always very useful and critical
which is great!<br>
<br>
<blockquote cite="mid:4C501509.7050908@sgc.ox.ac.uk" type="cite">the
2nd-last one of the validation pack, where you
recommend against the use of UNK atoms, but don't say why:<br>
<br>
<snip><br>
Some programs and people tend to interpret unknown density using
“dummy<br>
atoms”. In PDB files it typically looks like this:<br>
ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X<br>
ATOM 11 O UNK 2 6.994 -12.600 10.740 1.00 7.16 X<br>
ATOM 12 O UNK 2 6.028 -13.737 10.607 1.00 6.58 X<br>
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28<br>
ATOM 14 DUM UNK 2 5.099 -13.727 11.792 1.00 7.15<br>
- <b>Do not deposit this in PDB</b>, especially if chemical
element
type is undefined<br>
(rightmost column)<br>
</snip><br>
</blockquote>
<br>
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.<br>
<br>
The problems with records like:<br>
<br>
ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X<br>
ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 <br>
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28<br>
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28 X<br>
<br>
are:<br>
<br>
- 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;<br>
<br>
- 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;<br>
<br>
- 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);<br>
<br>
- 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)?<br>
<br>
- 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 -:)<br>
<br>
In summary:<br>
<br>
- do not put there anything hoping that future generation smarter
software will find out what it is;<br>
- 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).<br>
<br>
All the best!<br>
Pavel.<br>
<br>
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