pafonine at lbl.gov
Thu Mar 24 02:27:37 PDT 2011
> Yes, there are basically three options:
> 1) cut the side chain down to whatever is still visible in the density
> 2) let the refinement proceed as is
> 3) set side chain atom occupancies to zero
> Personally, I have evolved from 2) to 1). The argument was that
> omitting atoms will confuse some end users,
there can be endless list of things how you can confuse the end-user, so
I guess I put it aside and assume dealing with an educated individual.
> and refinement will
> essentially take care of it by increasing the B-factors.
Yes, stupid refinement would probably do it. phenix.refine will not do
it since zero occupancy atoms will not contribute to the scattering, and
their B-factors will be roughly similar to those of neighbor atoms.
> I have seen
> some quite convincing evidence since that the disordered side chains do
> have a detectable effect on the rest of the model, and thus leaving them
> in makes a model worse.
I've seen both.
> Other half of the argument was of semantic
> nature and referred more to replacing disordered residues with alanines,
> which is silly
It is silly but honest. If you call TYR something like this
ATOM 134 N TYR A 19 21.657 -76.614 65.963 1.00 28.50
ATOM 135 CA TYR A 19 23.064 -76.802 65.641 1.00 27.23
ATOM 136 CB TYR A 19 23.231 -77.079 64.157 1.00 30.04
ATOM 137 C TYR A 19 23.816 -75.537 66.027 1.00 27.07
ATOM 138 O TYR A 19 23.265 -74.434 65.976 1.00 24.32
that would be weird too. Call it then "handicapped TYR" -;) And I guess
to see something like this is confusing for the end user too (especially
one who learns things). If I see something like this my first geuss
would be "someone messed up the file while doing copy-paste".
> because we know from sequence it's not alanine
Yes, we know this. But before we really know this, we need:
1) extract sequence from PDB file;
2) get your correct sequence;
3) align them and see mismatches;
4) distinguish between model building (occasional) errors and
intentional ones (due to ALA truncation).
> The third option (the one you gravitate towards) seems problematic to me
> for the following reasons. The meaning of the occupancy is that the
> atom distribution in space is multimodal, and it spends certain fraction
> of time vibrating around the specified position. So what is the meaning
> of zero occupancy? This is the average atomic position, but it spends
> zero time here? Makes no physical sense, and in fact is wrong since
> there is some non-zero probability that the disordered side chain will
> occupy the designated conformation. Of course, structural model may be
> considered a *mathematical* model, and it does not have to be strictly
> interpretable (or interpretable the way I see most logical, anyway).
This is a valid argument, I agree. Better, one would need to run a bunch
of identical refinements and obtain the ensemble that would tell you
(more or less) the uncertainty and degree of confidence for each atom:
That would be a step forward towards a better option then setting the
occupancy to zero.
> As for end-user argument, I would say that omitted atoms are better than
> high B-factors or zero occupancies,
I exclude high b-factors as an option because if the program does it
then it is a bug that must be fixed.
I agree, making occupancy zero is kind of abusing it in order to say "I
do not see this atom". But so far I have no feeling about what is more
- set occupancy to zero in order to say "I don't see it in the map", or
- call TYR (or whatever else) something that is according to the atom
content is NOT TYR but is ALA.
Finally, when we model 4-6A or so resolution data why we stick atoms
into those tubes of density? Do these densities really tell you where
that specific atom or often even residue is?
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