[phenixbb] ls_wunit_k1

Jianghai Zhu jzhu at cbr.med.harvard.edu
Mon Mar 26 07:14:43 PDT 2007

I found the "automatic adjustment" in my log file.  It says that the  
target for bulk solvent correction and scaling is changed to  
ls_wunit_k1 and is required for the target mlhl.  Why is that?  for  
stability issues?


Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232

On Mar 26, 2007, at 12:41 AM, Ralf W. Grosse-Kunstleve wrote:

>> All right.  The target for my TLS is also LS.  Is that intentional  
>> too?
> Pavel, who wrote the TLS code, is current offline.
> I don't know if Pavel ran systematic tests to determine the default
> target for TLS.
> A couple of months ago I ran systematic tests exercising rigid body
> refinement using both the LS and ML targets. Overall it turned out  
> that
> ML is slightly better than LS. For an individual structure and a
> particular starting point it can be the other way around, but averaged
> over about 70 structures with 100 random starting points each ML
> generally outperforms LS. We should have updated the default
> accordingly, but it fell through the cracks.
> If you have the time to try out both ML and LS in the refinement of
> your structure, we'd be interested to know the results.
> Ralf
> P.S.: What's the version of phenix.refine you are using? -- I'm still
> puzzled why you didn't get the "automatic adjustment" messages.
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