On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote:
> Does anyone know if Molprobity has recently changed the standard bond lengths
> and angles that it uses ?
>
> Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond
> angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new
> structure refined with Refmac. I then tried Molprobity on a deposited PDB
> structure that also contains AMPPNP and it reported the same errors. I am
> sure that these errors were not reported when this structure (2JDI) was
> deposited in 2007.
>
> This would suggest that the standard dictionary that Molprobity uses has
> changed, but I cannot find any reference to this on the Molprobity pages.
>
> I would be very grateful if anyone can throw some light on this.
I suspect, though I cannot say for sure, that the difference is
whether ANP is [correctly] treated as a ligand or [incorrectly]
treated as a monomer in a nucleic acid polymer. We have seen
similar cases recently. For now I would say it is safe to
disregard Molprobity scores for ligands that just happen to be
nucleic acids.
Ethan
> Thanks,
>
> Andrew
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