[phenixbb] Clashes problem

Stephen Graham stepheng at strubi.ox.ac.uk
Wed Feb 13 03:25:28 PST 2008

Hi Pavel,

> 4) Also, clashes related concerns may be a result of inoptimal weight
> between Xray target and restrains. Although one can play with the weight
> adjusting scales manually by trying different values of "wxc_scale"
> parameter ("wxu_scale" is analog for b-factors refinement) the new
> version of phenix.refine has an automatic procedure for finding the best
> weight (here "the best" means the weight that leads to the lowest Rfree)
> (Carsten's suggestion). To use this option:
> % phenix.refine model.pdb data.mtz your_parameters.par optimize_wxc=true

Wouldn't it be better to try and get the highest Free Log Likelihood
Gain (LLG) rather than the lowest Rfree?  I would worry that trying to
optimise Rfree rather than LLG or even a free Rxpct (a-la BUSTER)
would be less stable/reliable.



Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

More information about the phenixbb mailing list