On the subject of missing residues: even if they're not included in the final reported structure, I think there is good reason to have them present (with occupancy zeroed as necessary) during refinement. It's exceedingly common to see structures where the 1-2 residues adjacent to an unresolved stretch have been allowed to twist into conformations incompatible with a continuation of the chain. Including the missing residues adds important stereochemical restraints to help keep them in check.
On the subject of sidechains: the first thing that many visualisation and/or modelling packages will do upon encountering a missing sidechain is to put it back - usually just by using a single set of stored internal coordinates, with no regard for clashes or electrostatics. If they're included by the crystallographer during model building, one would hope that there would be a generally stronger basis for their positioning.
Ultimately, it comes back to the need for a specific flag to clearly describe confidence in specific portions of the model, rather than relying on B-factor and occupancy values to provide some implicit guide.
Just my two cents.
Best regards,
Tristan
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
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> On 15 Nov 2015, at 9:25 am, Quyen Hoang <[log in to unmask]> wrote:
>
> Let's see if we can settle this. Ed might remember where I stood, but my view had changed a bit.
> 1. Delete atoms of a side-chain for which no density is visible if one is using density to find out what the residue looks like.
> 2. Model a complete residue even when density is missing for a side-chain atom if one is using the density to find the location of the residue.
>
> Can we settle with this?
>
> Cheers,
> Quyen
>
>
>> On Nov 14, 2015, at 5:40 PM, Ed Pozharski <[log in to unmask]> 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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