[phenixbb] Weight optimization

Pavel Afonine PAfonine at lbl.gov
Wed May 26 08:30:18 PDT 2010

Hi Jianghai,

> Yes, these limits fixed the problem.  

thanks for letting know, I'm glad it worked for you!

> But the default values should be 0.02 and 2, respectively, I believe.

Well, I guess better to have it resolution dependent, and best to have 
it local per bond or so. I have no intention to open another can of 
worms, but where those 0.02 and 2 come from? Can you really see that 
level of details at say 2.5A resolution and lower? I guess at that 
resolutions they should be both zero. In contrast, at higher resolution 
larger deviations are justified just by the data and so larger margins 
in restraints should be allowed. I know there is a heap of good papers 
on this matter, including the recent ones, and there are long threads on 
bb, but to me this question is still somewhat open. May be someone on 
the board can thoroughly/convincingly comment on this, summarizing all 
previous discussions?

Anyway, I agree, 0.05 and 3.5 is probably too generous.

All the best!

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