[phenixbb] weights optimization, add hydrogens
Pavel Afonine
PAfonine at lbl.gov
Tue Feb 23 10:40:03 PST 2010
Hi Ursula,
> I am refining a 2.0 A structure in Phenix using mostly the graphical
> interface. The maps are very good and the R factors are low
> (0.208/0.173). But the geometry is not so great with bond deviations
> of 0.208 and Angle deviations of 1.85. What is the best thing to do
> to try to improve the geometry. Should I try to optimize the weights?
the R-factors seem good indeed. Yes, Although the angle deviations seem
ok to me, I'm concerned about the bond deviations... Yes, you can try
two things:
- increase the restraints strength by increasing the corresponding weight:
from the command line: "wc=VALUE", where VALUE is a number somewhat
larger than 1.0;
from the GUI:
Refinement settings -> All parameters -> Refinement target weights...
-> Stereochemistry weight scale
- Run automatic weight optimization (note, this may take a while to run):
from the command line: use keyword: "optimize_wxc=true";
from the GUI:
Refinement settings -> All parameters -> Refinement target weights...
-> Optimize X-ray/stereochemistry weight
Alternatively, you can send me your PDB and data file and I will tell
you what exactly is not right and how to fix it.
Pavel.
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