That sounds like the bug in Phenix.refine v1.8 that a few of us encountered - updating to the latest release will help.
Actually wasn't so much a bug but a "feature", albeit not the best one imaginable. Anyone using older v1.8 versions should update.
---
Phil Jeffrey
Princeton
On Nov 2, 2012, at 6:41 AM, "Demetres D. Leonidas" <[log in to unmask]> wrote:
> Dear Tim,
>
> this affects all atoms and yes I did reset the B-factors to 20.00 prior to refinement. I have not tried REFMAC but now I will give it a try since phenix does not seem to do the job.
>
> best
>
> Demetres
>
>
> On 2/11/2012 1:34 μμ, Tim Gruene wrote:
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>> Dear Demetres,
>>
>> does this affect all atoms, or only a few selected ones?
>>
>> Did you compare with refmac5 (for e.g. input script errors), or did
>> you reset the B-factors to a reasonable value (e.g. 20-30) prior to
>> refinement? pdbset can do this conveniently.
>>
>> Best,
>> Tim
>>
>> On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote:
>>> Hello,
>>>
>>> I am experiencing a weird problem with B factor refinement
>>> (individual, isotropic) in phenix.refine (1.8.1.-1168) and a
>>> structure at 1.9 A resolution. The ADP values after the refinement
>>> are very very low, less than 2 and sometimes 0. I am getting the
>>> same result with and without optimization of the X-ray/ADP weight.
>>> Has anyone else noticed that and is there a workaround ?
>>>
>>> Demetres
>>>
>> - -- Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
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>
> --
> -----------------------------------------------
> Dr. Demetres D. Leonidas
> Associate Professor of Biochemistry
> Department of Biochemistry & Biotechnology
> University of Thessaly
> 26 Ploutonos Str.
> 41221 Larissa, Greece
> ---------------------------------------------
> Tel. +302410 565278
> Tel. +302410 565297 (Lab)
> Fax. +302410 565290
> E-mail: [log in to unmask]
> http://www.bio.uth.gr
> -----------------------------------------------
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