[phenixbb] Atoms with iso. B <=0

[Stephen Weeks]

Pavel and Nathaniel,
   I had the same problem with both phenix-1.8.1-1168
and phenix-1.8.2-1309. The current nightly build (phenix-dev-1334) worked
flawlessly. In fact the b-factors make a lot more sense across the  whole
structure now,  typically tripling the mean value and being in better
agreement with the statistics for structures of similar resolution.

Cheers

Stephen


On 5 April 2013 18:31, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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
>
>
> _______________________________________________
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
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