On 2 Oct 2008, at 09:11, Kay Diederichs wrote:
Phil Evans schrieb:
In the new coot, lots of my PDB files have all atoms coloured
white. Is this a consequence of the new PDB format conventions
Phil
Yes I think so - I found that PDB files that behave like that lack
the atom type in the last column (which might be req'd by the new
PDB format convention - no idea why).
The 4-character atom name did not allow well enough for unique
identification of the element type, especially with H atoms.
Overloading the atom name with element type causes a lot of problems.
Separating the atom type to another column allows for both atom type
and ionization state -- i.e. correct identification of the scattering
factor needed.
Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need
to know for both refinement and modeling.
Lynn Ten Eyck
running through pdbset fixes this easily.
best,
Kay
--
Kay Diederichs http://strucbio.biologie.uni-
konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax
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