good afternoon On Tue, Oct 8, 2024, 8:27 PM Pavel Afonine wrote:

Hi All,

yes, the docs are a bit behind. The current behavior is controlled by:

adp_individual_isotropic=Auto

You can find this by running:

phenix.real_space_refine --show-defaults=3 | grep adp

Here, "Auto" means the program decides whether to use individual or group isotropic ADPs, based on the resolution (group ADPs for resolutions worse than 3.5Å, and individual ADPs otherwise).

You can also set this manually:

adp_individual_isotropic=True to enable individual isotropic ADP refinement, or

adp_individual_isotropic=False to fall back on group ADP refinement.

Hope this helps clarify things a bit!

Pavel

On 10/8/24 00:20, Guillaume Gaullier wrote:

Hi Leonid,

The phenix documentation might be outdated. The documentation of ISOLDE has recommended running phenix.real_space_refine for a long time now, precisely to refine the atomic B-factors (that ISOLDE does not refine). I trust that Tristan (ISOLDE's author) would not recommend doing this if it didn't produce a correct result.

I hope this helps,

Guillaume ------------------------------ *From:* Leonid Sazanov *Sent:* Friday, October 4, 2024 4:48:56 PM *To:* PHENIX user mailing list *Subject:* [phenixbb] real space refine ADPs

Hi, according to online description phenix.real_space_refine should refine only group ADPs per residue. However, in practice after the run with ADP included in strategy the recent versions refine individual B-factors per atom. They seem to look OK, but I wonder if this is a beta feature or fully implemented by now? Many thanks Leonid

-- Prof. Leonid Sazanov FRS Institute of Science and Technology Austria (ISTA) Am Campus 1 https://www.google.com/maps/search/Am+Campus+1+%0D%0A++++++++++++A-3400+Klosterneuburg+%0D%0A++++++++++++Austria?entry=gmail&source=g A-3400 Klosterneuburg https://www.google.com/maps/search/Am+Campus+1+%0D%0A++++++++++++A-3400+Klosterneuburg+%0D%0A++++++++++++Austria?entry=gmail&source=g Austria https://www.google.com/maps/search/Am+Campus+1+%0D%0A++++++++++++A-3400+Klosterneuburg+%0D%0A++++++++++++Austria?entry=gmail&source=g

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