[phenixbb] rotamers

[Dale Tronrud]

On 3/24/2011 2:57 AM, Pavel Afonine wrote:
>
>> However I'm fairly sure though that if you deposit data in the PDB with zero occupancy atoms, the curators remove the atoms anyway
>> and stick them in one of the header comments - true?
>
> Interesting... I do not know whether it happens or not, but if it does happen then is really terrible. As the author of the
> structure I am responsible for its content, and if someone manipulates the structure I would not like to be responsible for it. So I
> guess this kind of manipulation (again, if it takes place) should be documented in PDB file header along with the name of the person
> who did it (well, in that case he or she becomes a co-author! -:) )
>
    The PDB does not modify the model in this way.  They will run their validation
checks on the deposited model and notify the depositor of anything thought to be
strange, including missing atoms, but if the depositor signs off on it the file
is put in the data base.

    This is a debate that goes back many years and the PDB has no interest in taking
sides.

    Personally I place atoms when I have some idea where to put them.  If someone
needs the full side chain to perform electrostatic calculations the method
probably would lead towards some favored method of placing the floppy bits
(perhaps taking into account the location of the other charges in the area).  If
someone needs to place atoms for a packing analysis, then they may want to create
placements for the disordered atoms, but would have different criteria for the
task then the person interested in electrostatics.  I am a crystallographer, not
a mind reader.  I look at density (and other information) and do my best to
build a model.

    Of the possible ways to represent this common situation I think placing a
side chain with occupancy set to zero is the worst.  For the naive user (and
that is not necessarly pejorative) it will lead them to view the placement of
those atoms as unwarrantably confident.  For those with a deep understanding
of the meaning of the parameters it is flat wrong - it says that I know that
this atom is never in this location.

    If you want to be precise for the knowledgeable user you need to put in
a non-zero occupancy but assign it a very large sigma on your SIGATM record
for that atom.  Of course when naive users see SIGATM records I expect their
heads will explode.

Dale Tronrud

> Pavel.
>
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