It turns out that Eugine Krissinel is way ahead of me - in mmdb he
provides a flag to fix up the missing elements.
This is non-optionally done now in 0.5.1-pre-1 and following versions.
Paul
Charlie Bond wrote:
How straightforward would it be to modify coot to automatically 'run
pdbset' on loaded pdb files to overcome this issue?
Cheers,
Charlie
Lynn F. Ten Eyck wrote:
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 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
.
