On 7/13/2012 1:58 AM, Tim Gruene wrote:
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Dear all,
I am surprised by the discussion about chiraliy of an utterly
centrosymmetric molecule. Shouldn't the four Oxygen atoms be at least
from a QM point-of-view to indistinguishable? What reason is there to
maintain a certain 'order' in the human-induced numbering scheme?
There are good reasons for maintaining order in this human-induced
numbering scheme. A common operation is to superimpose two molecules
and calculate the rmsd of the positional differences. This calculation
is not useful when the Val CG1 and CG2 are swapped in one molecule relative
to the other. Suddenly you have, maybe a handful, of atoms that differ
in position by about 3.5 A when most of us would consider this to be
nonsense. We want the rmsd between equivalent atoms regardless of the
human-induced numbering scheme. There are two ways this can come about.
1) The overlay program could swap the labels on one to match the other or
2) The labels can be defined to be consistent from the start.
Neither 1) or 2) are objectively better in any absolute sense. The
Powers that Be, however, have decided that for Val, Leu, Phe, Tyr, and
the PO2 in DNA, RNA, and many co-enzymes models should be adjusted to
conform to a standard. If we are doing this for these groups in order
to make comparison of models simpler, why stop there? If we say there
are standards for some groups but not others we have the worst of both
worlds - We have to both modify models and write complicated comparison
programs.
The failure of comparison programs to correct for labeling differences
is generally a silent error - A handful of 3.5 A differences mixed into
thousands of very small differences will not likely cause an increase in
the rmsd that would be noticed. Only if the individual differences are
plotted, or the biggest differences are listed will the user notice the
problem. Silent errors are the worst errors since they are the most
likely to make it all the way to publication.
As I see it, the problem here lies in the program that created the
original poster's SO4 group. If it had matched the convention now present
in the CCP4 cif there would be none of these problems. That program
should be tracked down and updated.
The problem of labeling groups that have symmetry along a rotatable
torsion angle is a persistent problem that, I'm afraid, has no permanent
solution other than CONSTANT VIGILANCE. I see that the newer versions
of Coot have taken up this burden, at least for Phe and Tyr. (I guess
we need a picture of a coot with one big roving eye.)
Since we are already unambiguously defining the labeling for a number
of the groups we use, I think it is up to you to justify why this group
should be treated differently.
Dale Tronrud
P.S. On a only slightly off topic note - I'm quite afraid of using both
as the definition for chirality. I've noticed that this keyword is used
as an excuse to not figure out what the real chirality of an atom is and
as a result people build models with bad chiral centers that are not flagged
by their software (another silent error that makes it to publication.) The
PDB is littered with cofactors and ligands that have inverted chiral centers
(Even centers that Pasteur would approve). I would prefer that both
was not a legal value and researchers would be required to think about
chirality.
Cheers,
Tim
On 07/13/12 00:22, Dale Tronrud wrote:
While this change has made your symptom go away it is stretching it
a bit to call this a fix. You have not corrected the root
problem that the names you have given your atoms do not match the
convention which is being applied for SO4 groups. Changing the cif
means that you don't have to worry about it, but people who study
such details will be forced to deal with the incorrect labels of
your model in the future.
Wouldn't it just be easier to swap the names of two oxygen atoms in
each SO4, leaving the cif alone? Your difficulties will go away
and people using your model in the future will also have a simpler
life.
This labeling problem is not new. The fight to standardize the
labeling of the methyl groups in Valine and Leucine was raging in
the 1980's. Standardizing the labels on the PO4 groups in DNA/RNA
was much more recent. It helps everyone when you know you can
overlay two models and have a logical solution without a rotation
matrix with a determinate of -1.
Besides, you will continue to be bitten by this problem as you use
other programs, until you actually swap some labels.
Dale Tronrud
On 07/12/12 15:00, Joel Tyndall wrote:
Hi all,
Thanks very much to all who responded so quickly. The fix is a
one liner in the SO4.cif file (last line)
SO4 chir_01 S O1 O2 O3both
which I believe is now in the 6.3.0 release.
Interestingly the chirality parameters were not in the SO4.cif
file in 6.1.3 but then appeared in 6.2.0.
Once again
