Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated? -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: [email protected]
TLS refinement results in an anisotropic b-factor component per atom. You then add to this the individual atomic isotropic b-factor and you’ll get something that’s still anisotropic — that’s what’s stored in the ANISOU records.
Thanks,
Nick
On 31 May 2018, at 08:52, Eugene Osipov
Some reading suggestions that should help (I'm not claiming this is a complete list of relevant resources!!!): 1) TLS from fundamentals to practice. Urzhumtsev A, Afonine PV, Adams PD. Crystallography Reviews 19, 230-270 (2013). 2) From deep TLS validation to ensembles of atomic models built from elemental motions. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD Acta Cryst. D71, 1668-83 (2015). 3) "On atomic displacement parameters (ADP) and their parameterization in PHENIX" http://phenix-online.org/newsletter/CCN_2010_07.pdf 4) http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf Towards automated crystallographic structure refinement with phenix.refine. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Acta Cryst. D68, 352-367 (2012). Pavel On 5/31/18 15:49, Eugene Osipov wrote:
Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated?
-- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: [email protected] mailto:[email protected]
Pavel, Nick,
Awesome, thanks!
чт, 31 мая 2018 г., 12:00 Pavel Afonine
Some reading suggestions that should help (I'm not claiming this is a complete list of relevant resources!!!):
1) TLS from fundamentals to practice. Urzhumtsev A, Afonine PV, Adams PD. Crystallography Reviews 19, 230-270 (2013).
2) From deep TLS validation to ensembles of atomic models built from elemental motions. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD Acta Cryst. D71, 1668-83 (2015).
3) "On atomic displacement parameters (ADP) and their parameterization in PHENIX" http://phenix-online.org/newsletter/CCN_2010_07.pdf
4) http://journals.iucr.org/d/issues/2012/04/00/ba5180/ba5180.pdf Towards automated crystallographic structure refinement with phenix.refine. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Acta Cryst. D68, 352-367 (2012).
Pavel
On 5/31/18 15:49, Eugene Osipov wrote:
Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated?
-- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: [email protected]
participants (3)
-
Eugene Osipov -
Pavel Afonine -
Pearce, N.M. (Nick)