[phenixbb] help with geometry target weight

Pavel Afonine PAfonine at lbl.gov
Thu Mar 18 14:10:00 PDT 2010

Hi Breann,

> I am currently refining a structure at 2.4A resolution. I would like to increase the geometry target weight during refinement, however when I decrease wxc_scale (to 0.25 or 0.1) there is no change in the bond deviations or R factors compared to refinement with the default wxc_scale. I noticed in the refinement logfile under XYZ refinement wc=0. This does not change when I change the wc value in the command line (wc=2.0 for example) as suggested in a previous email. I also see no change when I use the optimize_wxc=true command. Examples of the command line input and output log files are below. I am currently using version 1.6-289 and would appreciate any help in resolving this issue as it seems the geometry is not being properly weighted during refinement.

what you describe is extremely weird. The restraints weight scale, wc, 
is set to 1.0 by default and is never adjusted automatically unless you 
explicitly specify a value from the command line or a parameter file. 
So, I have no idea why you end up having wx=0.

The only way I can find this out if you send me the model, data, cif 
files (if any), parameter files (if any) and the exact command you run, 
so I can reproduce the behavior you see and tell what happens.


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