ALERT:MolProbity will be DOWN from Wednesday, January 28 8PM EST to Thursday, January 29 8AM EST for building electrical work.
MolProbity4 structure validation now provides many of its validation metrics through CCTBX, the open-source component of the Phenix crystallographic package. CCTBX allows for consistent validation results with Phenix, as well as added functionality, such as geometry regularization of NQH flips. Read more about this change here.
We have updated Reduce to add hydrogens at a length more consistent with electron-cloud positions, and accordingly adjusted the Van der Waals radii in Probe to compensate for the change. This will affect comparison of results calculated with older versions of MolProbity, but generally results in lower clashscores. For analyses using nuclear-position hydrogens, you have the option of selecting nuclear x-H positions when adding hydrogens. Read more about this change here.
Ramachandran scoring has also been updated to use new six-category distributions, derived from a larger
Top8000 dataset of high quality PDB files.