[phenixbb] question on bad geometry

MARTYN SYMMONS martainn_oshiomains at btinternet.com
Wed Sep 1 04:49:45 PDT 2010


This is a good point and it is often useful to prune back to poly(ALA) in doubtful regions which can help centre the backbone in the strongest density and then re-build sidechains afresh.

All the best
           Martyn 

Martyn Symmons
Cambridge UK

--- On Wed, 1/9/10, Robert Immormino <immormino at gmail.com> wrote:

> From: Robert Immormino <immormino at gmail.com>
> Subject: Re: [phenixbb] question on bad geometry
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Date: Wednesday, 1 September, 2010, 12:27
> Hi Fengyun,
> 
> Statistics like these mean that the backbone of your model
> is not
> quite right, so re-building is necessary.  And Pavel
> can correct me if
> I'm wrong, but I think fix_rotamer becomes increasing less
> successful
> the further you have backbone from the correct
> position.  So first the
> mainchain and then the sidechains need to be fixed.
> 
> Do the Ramachandran outliers bunch together in loop
> regions, or are
> they distributed across the structure?
> 
> Most of the Ramachandran outliers in secondary structure
> regions in my
> experience are due to having the peptide bond
> flipped.  Check closely
> to see if you can find density for carbonyl oxygens, and
> remember in
> alpha structure they point toward the C-terminus, and in
> beta
> structure they alternate.
> 
> Loops are more difficult.  The only general rule I
> know is that
> consecutive carbonyls tend to not point in the same
> direction....with
> the major exception being metal binding loops.
> 
> Also it may be worth double checking the sequence register,
> especially
> near ends of secondary structure elements.
> 
> Autobuild likely will take care of most of your issues, but
> a careful
> eye toward rebuilding can give you confidence that you've
> got the
> model right.
> 
> Good Luck,
> -bob
> 
> 
> On Tue, Aug 31, 2010 at 9:37 PM,  <fn1 at rice.edu>
> wrote:
> > Hi everyone,
> >
> > I have a structure at 2.3 A refined in phenix to
> R/Rfree=0.23/0.28. However,
> > the geometry is not that good, the followings are the
> output from
> > phenix.model_vs_data,
> >
> >    Stereochemistry statistics (mean, max, count):
> >      bonds            :   0.0080   0.0547
> 3244
> >      angles           :   1.1669  12.1085
> 4374
> >      dihedrals        :  15.7241  85.6280
> 1202
> >      chirality        :   0.0706   0.2831
> 536
> >      planarity        :   0.0036   0.0246
> 573
> >      non-bonded (min) :   2.1217
> >      Ramachandran plot, number of:
> >        outliers : 17    (4.02  %)
> >        allowed  : 37    (8.75  %)
> >        favored  : 369   (87.23 %)
> >      Rotamer outliers        : 30 (8.62 %)
> goal: < 1%
> >      Cbeta deviations >0.25A : 0
> >      All-atom clashscore     : 40.51 (steric
> overlaps >0.4A per 1000 atoms)
> >
> > I tried to use fix_rotamer=True, but it doesn't help
> at all. As to the
> > rotamer outliers, the value is far higher than the
> ideal one. Does that mean
> > I need to manually adjust the model? Or will autobuild
> help improve the
> > geometry?
> >
> > Thanks!
> > Fengyun
> >
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> >
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