All un-fsck options should be non-default optional, lest they create
other problems.
On Oct 2, 2008, at 6:27 PM, 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: [log in to unmask] Tel +49 7531 88 4049 Fax
>>> 3183
>>> Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457
>>> Konstanz
>> .
>
> --
> Charlie Bond
> Professorial Fellow
> University of Western Australia
> School of Biomedical, Biomolecular and Chemical Sciences
> M310
> 35 Stirling Highway
> Crawley WA 6009
> Australia
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