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
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--
Charlie Bond
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University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
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Australia
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