[phenixbb] Problem with Molprobity analysis in phenix 1.6.4

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Tue Oct 5 18:32:27 PDT 2010

Hi Nat,

After the long discussion, mostly on CCP4BB, about riding H,
which covered different H-bond lengths, it would be really
good if the GUI and other Phenix documentation explained
exactly how this is handled. 

I think using riding H as a geometry restraint during refinement
should be standard practice, but I think 'interpreting' those H atoms
in all but the very highest resolution X-ray structures is probably
not good. 

From: Nathaniel Echols [nechols at lbl.gov]
Sent: Tuesday, October 05, 2010 3:56 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Problem with Molprobity analysis in phenix 1.6.4

On Tue, Oct 5, 2010 at 11:53 AM, Mark A Saper <saper at umich.edu> wrote:
> 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?

There is a discrepancy in hydrogen bond lengths in Reduce versus the
monomer library - I believe Reduce is using the distance to the center
of the nucleus instead of the center of the electron cloud.
phenix.refine will regularize the hydrogen geometry before refining
the non-hydrogen coordinates, so it is correcting the bond lengths to
be appropriate for X-ray refinement.  It looks like they're getting
stripped off and replaced when we run the clashscore calculations, so
you end up with the longer bonds and thus more clashes.  I think the
consensus among the group was that these are more appropriate for
interpreting (instead of refining) the model, but I'll double-check
this with everyone.  The GUI could at least be more explicit about how
the calculations are done, however.

(By the way, a clashscore of 8.69 is pretty decent anyway.)

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