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: [log in to unmask] Tel +49 7531 88 4049 Fax 3183
>>> Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
>>
>> .
>>
>
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