[phenixbb] Problem with Molprobity analysis in phenix 1.6.4

Florian Schmitzberger schmitzberger at crystal.harvard.edu
Wed Oct 6 06:56:41 PDT 2010

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.



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

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