[phenixbb] geometry weight and rmsd bonds - angles

Nathaniel Echols nechols at lbl.gov
Thu Aug 12 08:23:11 PDT 2010

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.

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