On 15/09/14 18:05, Dale Tronrud wrote:
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On 9/15/2014 9:42 AM, Andrew Leslie wrote:
Dear Huw,
Many thanks for this information. I had seen the notice about
Molprobity using CCTBX validation metrics, but I mistakenly thought
that Phenix used the CCP4 monomer library, which I think was true
once but is clearly no longer the case.
Given the very small sigma values associated with the Phenix C4-C5
bond length, it could be said to differ by 10.4 standard deviations
from the CCP4 monomer library value !
Many thanks to all others who have responded too.
In response to Dale's comment, the frustrating thing is that this
is not interesting at all, it is merely confusing. The resolution
of the new structure is only ~3 Å, so there is no way that one can
make meaningful statements about distortions from standard
geometry. The warnings merely highlight the fact that we do not
have adequate library entries.
One wonders what is meant by "we" here? LMB? CCP4 users? Macromolecular
crystallographers (that also use Phenix)? Each of these constituencies
would give a different response...
Which is interesting. ;-)
To be serious, I do think this is interesting. Apparently someone
looking at this molecule has decided that this bond should be 1.49 A
with a sigma of 0.02 A while someone else looking at the same molecule
concluded it should be 1.386 A with sigma 0.01 A.
Which is strange. I'd imagine that the refmac monomer library was
constructed by libcheck. The input bond order is "double" - but a decent
dictionary generating program would determine that this is actually
aromatic - and thus should pick up the distance for an aromatic
CR56-CR56, i.e. 1.38 (0.02)A. In this case, this has not happened and
(it seems to me) that the value for a single bond has been used instead,
i.e. 1.49 (0.02)A.
The most
significant source of uncertainty in this target value (whether it is
a double bond or an aromatic bond) has been ignored. Each library is
constructed ignoring the possibility of error in categorizing the type
of bond.
It seems so. But is that so bad? In this case, is there really any
doubt that this bond order should be "aromatic"?
I think the lesson is that the sigmas are being seriously under
estimated when the target values are not derived from real high
resolution structures.
I would have said the opposite - the Refmac monomer library usually
overestimates the esds compared to the distributions from small molecule
crystal structures (I am presuming that the bond orders are unambiguous).
Isn't it also interesting that the double bond of ccp4 is longer
than the aromatic bond of phenix? Not what I would have expected.
Nor I. I suspect a bug in libcheck.
For the record, the results from pyrogen are:
ANP C5 C4 aromatic 1.38494 0.0198269 # pyrogen
c.f
ANP C5 C4 aromatic 1.388 0.011 # grade
ANP C5 C4 N3 126.78 1.33586 # pyrogen
c.f.
ANP C5 C4 C3 126.8 0.7 # grade
(I could trim the sfs a bit, I suppose, hmmm...)
Paul.
