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. Thanks, Andrew
