[phenixbb] Weight optimization
PAfonine at lbl.gov
Fri May 28 22:58:31 PDT 2010
I have no quick answer. I will have a look within next few days and let
you know. It may be a side effect of runtime optimization - I'm trying
to save some refinement runs by looking at the available accumulated
statistics and extrapolating from that. Anyway, I guess it's time to
review that code (given the amount of usage). May be it is safer to give
up some runtime over the robustness and predictability... will see.
Have a great week-end!
On 5/28/10 9:41 PM, Jianghai Zhu wrote:
> After a few trials, looks like the angles_rmsd_max cannot be set to a value lower than 1.0. Everytime I did that, the values for bonds_rmsd_max and angles_rmsd_max reverted to the default numbers in the refinement and the limits I set in the input file are not effective. How do I fix that? Thanks.
> -- Jianghai
> On May 26, 2010, at 11:30 AM, Pavel Afonine wrote:
>> 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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