[phenixbb] geometry weight and rmsd bonds - angles

[Pavel Afonine]

  Hi Lionel,

something I forgot to mention/ask: if you are using a CIF file for your 
ligand that was created by ProDRG then I would strongly recommend using 
phenix.ready_set or eLBOW to get a new CIF file and use it from now on 
with phenix.refine. We had a lot of problems with nonsensical ProDRG 
created CIF files in the past and still runinng into them from time to time.

The command

phenix.ready_set model.pdb

will create a CIF file for use in refinement.

Pavel.



On 8/12/10 8:11 AM, 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 
> <mailto: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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