[phenixbb] Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)

Oliv Eidam eidamo at blur.compbio.ucsf.edu
Mon Mar 4 16:48:26 PST 2013


Update: I re-run refinements using phenix-dev-1314 (nightly build from 
2013-03-04) and the B-factors are now as expected (Bave ~20). Fwiw, it 
was necessary to reset all isotropic B-factors to 20 in the starting model.

Thanks a lot for fixing this, Pavel.

   Oliv


On 03/01/13 13:02, Pavel Afonine wrote:
> Hi Phil,
>
> this was the "odd special case" that is now (in next nightly build) 
> covered. I don't know how often such case happens but it escaped me 
> when I was implementing the original fix (sometime last summer).
>
> Pavel
>
> On 3/1/13 12:54 PM, Phil Jeffrey wrote:
>> Hello Pavel,
>>
>> Could you give us some idea if this was some odd special-case 
>> situation or if there is some lingering issue with scaling in 1.8* 
>> and we should all be planning on updating. (e.g. I'm using 
>> phenix-1.8.1-1168).
>>
>> Thanks
>> Phil Jeffrey
>> Princeton
>>
>> On 3/1/13 3:29 PM, Pavel Afonine wrote:
>>> Hello,
>>>
>>> anyone who experienced similar problem please get next available 
>>> nightly
>>> build version of Phenix (any version that is newer than today's one,
>>> which should be available in a day or a few days), and that should fix
>>> this problem. Please let me know otherwise.
>>>
>>> Pavel
>>>
>>
>>
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>
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-- 
Oliv Eidam, Ph.D.
Postdoctoral fellow

University of California, San Francisco
Dept. of Pharmaceutical Chemistry
1700 4th Street, Byers Hall North, Room 501
San Francisco, CA 94158 - Box 2550

Phone: 415-514-4253
Fax  : 415-514-4260
Email: eidamo at blur.compbio.ucsf.edu





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