Re: [phenixbb] Problem with Molprobity analysis in phenix 1.6.4

Dear Mark, I would be quite interested in opinions about the usage and assignment of hydrogens in the riding position for refinement too, especially at low resolution of around 4 A. How important are they for obtaining reasonable geometry at that resolution? From what I could see in the phenix manual hydrogens should should not be included into NCS or TLS groups and are automatically excluded from them. Cheers, Florian On Oct 5, 2010, at 9:32 PM, Mayer, Mark (NIH/NICHD) [E] wrote:

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.

Mark ________________________________________ From: Nathaniel Echols [[email protected]] 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 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.)

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602