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.

Pavel

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The phenix documentation might be outdated.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 <[email protected]>
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
A-3400 Klosterneuburg
Austria

Phone: +43 2243 9000 3026
E-mail: [email protected]
_______________________________________________
phenixbb mailing list -- [email protected]
To unsubscribe send an email to [email protected]
Unsubscribe: phenixbb-leave@%(host_name)s

VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

_______________________________________________
phenixbb mailing list -- [email protected]
To unsubscribe send an email to [email protected]
Unsubscribe: phenixbb-leave@%(host_name)s