OK, here we go again.
This has been argued ad nauseam, see for example
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(hard to believe we have gone more than a year without another version
of "what to do with disordered side chains" 250-post long discussion :)
I do not have much to add to the above, however
On 11/09/2012 05:22 PM, Matthew Franklin wrote:
> I think we can all agree that virtually every structure in the PDB
> will have a few residues where some of the atoms are not visible in
> the density. So the "trim the side chains" crowd is a
> well-represented minority at 30%, but 70% of depositors chose another
This maybe the historical average, I suspect that currently the "trim
the side chains crowd" may be at least at 50% (but what about Ohio? :).
Majority, however, is not always right (don't get me started on
> I personally like to leave all atoms on the side chains; they look
> wrong to me when beheaded. I just try to put the invisible atoms in a
> stereochemically plausible conformation, leave the occupancy set to 1,
> and let the refinement program deal with them.
With all due respect, to model something where there is no density (aka
experimental evidence) cannot be justified by aesthetics. On the
contrary, there is some evidence suggesting that modelling disordered
side chains in the way you describe adds small, but detectable error to
the rest of the model.
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs