[phenixbb] geometry weight and rmsd bonds - angles

Ed Pozharski epozh001 at umaryland.edu
Thu Aug 12 09:57:23 PDT 2010


0.022A rmsd on bonds seems to be a reasonable value at 1.3A.

On a different but related note, is there some way to print out the list
of bond length deviations from ideal values for all the restrained bonds
in the structure?  If yes, could you do me a favor and forward me such
list for you model?  Off-list of course, but I promise to post the
findings (assuming that they are interesting).

Ed.

On Thu, 2010-08-12 at 17:11 +0200, Lionel Costenaro wrote:
> 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.
> 
> Lionel
> 
> 
> 
> 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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> 
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