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 <
[email protected]> 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
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