[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
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
More information about the phenixbb
mailing list