[phenixbb] Atoms with iso. B <=0
Pavel Afonine
pafonine at lbl.gov
Fri Apr 5 09:31:24 PDT 2013
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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