Dear John,
there may be reasons to disagree with both options. This has been a
recurring discussion for many years, and in my mind the most convincing
arguments for both sides are as follows:
"Keepers":
I know the side chain is there and the high ADP is a good approximation
of reality. Removing atoms causes such a mess for the end user.
"Deleters":
We don't model missing loops, termini, ligands and waters when there is
no density, and side chains should not be treated differently. Most end
users think ADP is a nucleotide and will over-interpret the model.
I am a "keeper" when it comes to end user treatment, but a recently
converted "deleter" when it comes to modeling (a rather stressful
position). So I am not taking sides really, but rather looking for a
middle way. (Have to admit that my secret goal was to knock down the
zero occupancy fallacy :)
Perhaps these ideas are worth exploring:
1. Provide dual representation - a crystallographic model and an
end-user model, both downloadable from the PDB.
2. Model missing side chains "NMR-way"
3. A new data file format is needed (mmCIF?) that combines atomic model
with electron density, and visualization/analysis software shall be
modified to always utilize the experimental data
4. Implement reduced ADP restraints for disordered side chains to
further reduce model bias
But ultimately, as long as experimental data is deposited, I believe
that people are free to interpret their data the way they see fit.
Others are then free to look at the electron density and become outraged
at the interpretation.
Cheers,
Ed.
On Thu, 2011-03-31 at 23:25 +0100, Jrh wrote:
> Dear Ed,
> Thankyou for this and apologies for late reply.
> If one has chemical evidence for the presence of residues but these
> residues are disordered I find the delete atoms option disagreeable.
> Such a static disorder situation should be described by a high atomic
> displacement parameter, in my view. (nb the use of ADP is better than
> B factor terminology).
> Yours sincerely,
> John
> Prof John R Helliwell DSc
>
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
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