Currently, this discussion flames up every 1-2 years in the CCP4BB. When the PDB would impose some rule about what to include or not to include in the coordinate file, the discussion would probably flame up every 2nd PDB submission by some author from the opposing camp that does not agree with this rule.
What the validation task force could do is either recommend a "bouquet of side chains" as James Holton proposed, or introduce a "validation factor" next to the occupancy and B-factor, indicating how well the atomic position is supported by the experimental X-ray data.
My 2 cts,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Frank von Delft
Gesendet: Montag, 16. November 2015 04:41
An: [log in to unmask]
Betreff: Re: [ccp4bb] proper modeling of residues into patchy electron density
Strikes me the problem lies with semantics (in the true sense): the semantic meaning of each element of a PDB (or mmCIF or whatever) file has simply not been defined thoroughly enough, including the absence of something.
Hence the proliferation of words like "it means" and "I am saying" etc in posts like this one. It does not really matter what anybody (including Ed) thinks they mean by doing or not doing something; what matters is that everybody else can know that that is what they meant.
Which in this case clearly does not apply, else we'd not be having this thread, AGAIN.
Maybe one for the PDB validation task-force?
phx
On 14/11/2015 22:40, Ed Pozharski wrote:
> On 11/14/2015 04:36 PM, Artem Evdokimov wrote:
>>
>> I would agree with both sides, since absence of evidence is not
>> evidence of ansence.
>>
> Well, that's agnostic :)
>
> Just a comment - omitting side chain atoms from the model does not
> assert that they are somehow missing from the chemical structure one
> is modeling. It means that their spatial distribution cannot be
> adequately approximated from experimental data via simple 3D gaussian.
> So when I am excluding atoms from disordered side chains, I am not
> saying that an X-ray fairy has cut off covalent bonds with a tiny
> magic chainsaw. I am just saying I don't have sufficient experimental
> evidence to locate these atoms.
>
> Cheers,
>
> Ed
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