[phenixbb] Atoms with iso. B <=0

[Pavel Afonine]

Hi Stephen,

please use recent Phenix version and the problem will go away:

http://www.phenix-online.org/download/nightly_builds.cgi

Pavel

On 4/5/13 7:44 AM, Stephen Weeks wrote:
> Dear phenixBBers
>
>      I have a curious case of refinement of a 2.6 Angs structure, 
> where some of the atoms have a calculated b-factor of 0.00.  It seems 
> to be somewhat random where this occurs and includes atoms within the 
> backbone e.g. the nitrogen in the following residue:
>
> ATOM   2014  N   THR A 264      -2.685  42.357 -35.833  1.00  0.00     
>       N
> ATOM   2015  CA  THR A 264      -3.952  41.776 -35.425  1.00  1.50     
>       C
> ATOM   2016  CB  THR A 264      -4.684  41.052 -36.593  1.00  1.70     
>       C
> ATOM   2017  OG1 THR A 264      -4.077  39.772 -36.846  1.00  2.24     
>       O
> ATOM   2018  CG2 THR A 264      -4.669  41.867 -37.855  1.00  1.72     
>       C
> ATOM   2019  C   THR A 264      -3.687  40.729 -34.368  1.00  2.42     
>       C
> ATOM   2020  O   THR A 264      -2.571  40.210 -34.263  1.00  2.63     
>       O
>
> The structure contains 4 NCS related monomers but with a quick glance 
> I don't see any obvious correlation between each one as to which atoms 
> are  0.00. I did use phenix.pdbtools to randomise the B-factors (no 
> atoms had a value 0.00 afterwards) but  upon repeating  the refinement 
> the same problem occurs.
>
> Does anyone have a suggestion how to fix this ?
>
> Cheers
>
> Stephen
>
>
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