[phenixbb] geometry weight and rmsd bonds - angles

Lionel Costenaro lcocri at ibmb.csic.es
Thu Aug 12 08:11:30 PDT 2010

Hi Ralf,

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.


2010/8/12 Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>

> Hi Lionel,
> > wxc_scale (from default 0.5 downto 0.015),  wxu_scale (from default 1
> down
> > to 0.03), wc (from default 1 up to 8), with and without optimising wxc
> wxu.
> > Whatever the parameters, phenix never reached final rmsd better than
> 0.022
> > and 2.2.
> The first thing I'd check is the phenix.refine log with the list
> of worst restraints. Look for "Sorted by residual". Without
> having seen your structure, my first suspect would be problems
> with the ligand restraints or the covalent link to the protein.
> Ralf
> _______________________________________________
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> phenixbb at phenix-online.org
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