[phenixbb] weights optimization, add hydrogens

[Pavel Afonine]

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.