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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