I am running phenix 1.6.4-486 with GUI and obtained high clash scores in the Molprobity calculations done by phenix.refine.  I think I know why after doing some experiments with the current Molprobity running at http://molprobity.biochem.duke.edu/.

If I take my well-refined structure as output by phenix (.pdb) and use it directly on the Molprobity web site, the clash score is much lower: 2.75 for 39 total bumps.  Many of these involve residues or waters with high B factors.

If I first remove all hydrogens from the phenix-refined .pdb file with a text editor, and upload it to the Molprobity web site, then add hydrogens, and then calculate clash score, the score is now 8.69 or 123 bumps for 14150 atoms.  This is *identical* to what phenix calculates.  Therefore, why doesn't phenix feed the refined coordinates directly into the Molprobity (probe) calculations?  Has this change been made in one of the nightly builds?

Thanks,

Mark