[phenixbb] geometry weight and rmsd bonds - angles

[Nathaniel Echols]

On Thu, Aug 12, 2010 at 8:11 AM, Lionel Costenaro <lcocri at ibmb.csic.es>wrote:

> Indeed some bond length or angle restraint outliers are from the ligand
> when refining with phenix.
> However I don't think this is the problem, I give to refmac and phenix the
> same ligand dictionary (cif file from ProDRG with link definition added with
> JLigand). Refmac / phenix give me the following outliers >4 sigma : bond
> length 0 / 6, bond angle 0 / 23, dihedral 23 / 13, chiral 0 / 0, plan 3 /13.
> Clearly phenix is not doing a good job (R decrease, but not Rfree).
> For refmac I'm using an x-ray weighting term (matrix) of 0.8, which is more
> or less expected for 1.3A resolution.
> I don't really know how to fix the weights in phenix as I never used it
> before and did not find any hint in the manual or bb.
>

ProDRG's CIF files can be problematic, because they often have ESDs that are
inappropriately low and this confuses the minimizer.  I'd recommend running
phenix.elbow or phenix.ready_set to generate a new CIF file.

Other comments:
- Are you adding hydrogen atoms?  This can help with the geometry (and at
this resolution, it will certainly help with the R-factors).
- As pavel mentioned, you should turn on the weight optimization, but I
would also recommend setting the max allowable RMS(bonds) and RMS(angles) to
something more reasonable than the defaults - say, 0.02 and 2.0, if not
less.  (I forget the parameter names but if you are using the GUI they are
all in the same dialog window.)
- You should also update to version 1.6.4.

-Nat
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