[phenixbb] optimizing weights

Alexandra Deaconescu deacona at brandeis.edu
Wed Apr 20 12:21:19 PDT 2011

Dear all:

I would like to optimize my weights during Phenix refinement. I am running
Phenix 1.6.4-486 using the gui, and I have checked the "optimize weights",
but I cannot see the results of the optimization in the output, so I do not
know the relationship between Rfree/geometry and wc and wxc_scale (I might
not want to pick the automatically selected wxc_scale for the lowest Rfree,
but would like to find a reasonable values to give me good geometry). Some
earlier posts indicated that this is not output in the log file, but I am
running a more recent version...

Also, in case I wanted to adjust the weights manually, do I have set
wxc_scale AND check the   fix wc at the same time in the gui? Or just one of
them? What would be typical values to start with at 2.8A (even if the answer
depends on the particular data)?

Same question for the ADP refinement.... I am working at 2.8A and my B
factors are high (higher I think than what one would expect at this

Thanks for your help,

Alexandra M. Deaconescu, Ph.D.
Research Associate, HHMI
c/o Grigorieff Laboratory
Rosenstiel Center MS029
Brandeis University
415 South St.
Waltham, MA 02454

phone: 781-736-2498


Brandeis University
Kalman Receiving Dock
415 South St.
Waltham, MA 02454
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