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Hi Juergen,
This seems to me like a perfect case of "don't worry about it". obviously you
know the cause of the apparent "problem", namely that different parameter sets
are used. you may want to include a short remark in your pdb header, but that's
all I think is necessary. even if there would be just one parameter set, say the
Parkinson, but you have clear evidence from your density that you should remove
a certain restraint, do it. most of those parameter sets are derived by
statistical analysis of solved structures and they can only get better over time
if structures that contradict them get deposited.
My 2 cents,
Jens
P.S.: I don't understand you last comment. Why is the weight dependent on having
alternate conformations?
Juergen J. Mueller wrote:
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Dear all,
recently this item has been discussed here but I miss the summary.
Here my problem:
1. The CCP4 bond length/ bond angle library for DNA/RNA is taken from
Saenger-Book 1983.
2. The CNS library is taken from Parkinson et al. (1996) Acta Cryst.
One outcome from the last discussion was : It is not allowed to restrain
the sugar pucker
to C2' endo/exo...as it happens in XPLOR/CNS. That is also supported by
our own
finding: We got 5% better R-values (I know, the better structure is the
aim!) for a DNA
switching from CNS to REFMAC5.
But:
The only check of DNA/RNA stereochemical quality at the PDB is done by
WHATCHECK,
and WHATCHECK is based on the Parkinson data. In our case such a quality
check
results in 5-6 sigma deviations for bond angles in the DNA-backbone
which was
refined with REFMAC5.
What library can be recommended? Or, what can be done to improve the
1.6A structure?
Changing from WT=0.3 to higher values will not work, because the
complete DNA molecule has
an alternate conformation.
Thank you in advance,
Juergen
