[phenixbb] Atoms with iso. B <=0
Stephen Weeks
sd.weeksy at gmail.com
Fri Apr 5 14:47:21 PDT 2013
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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