before modelling a long side-chain in non-existing or dubious density,
also make sure it is really there in the protein by sequencing your
expression plasmid. Your arginine (for example) may in fact be a
serine or glycine...databases are not 100% accurate and neither is PCR
if it was used in the cloning.
Quoting Ed Pozharski:
> OK, here we go again.
>
> This has been argued ad nauseam, see for example
>
> http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
> or
> [log in to unmask]" target="_blank">http:[log in to unmask]
>
> (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 option.
> 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-over-sigma ratios).
>
>> 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.
>
> Cheers,
>
> Ed.
>
> --
> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
> Julian, King of Lemurs
>
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de BiotecnologĂa - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: [log in to unmask]
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