DEN restraints and ECHT disorder models

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 [email protected]

Hi Roberto, What’s described in the paper you refer to was done outside of Phenix, and I wasn’t even aware of this work. I'd check the "Availability" section: https://journals.iucr.org/d/issues/2021/11/00/qn5002/index.html and follow up with its authors if needed. The original implementation of ensemble refinement in Phenix as described here: https://elifesciences.org/articles/00311 is available in Phenix as outlined in that paper, and it hasn’t changed much since 2012. All the best! Pavel On 4/7/25 08:18, Roberto Battistutta wrote:
Dear all,
From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)?
Thank you very much,
Roberto.

Hi Roberto,
The changes to ensemble refinement (DEN, etc) should be available from any version of Phenix since ~Oct 2021 (https://github.com/cctbx/cctbx_project/commit/43bd136e4edce123ecc62197024f2e...)
N.B. this doesn't include the calculation of the Echt TLS B-factor model. If you want to use those you can get Echt separately here:
https://pandda.bitbucket.io/pandemic/echt.html
Please then set the "import_tls_pdb" parameter to the path of PDB output from Echt.
All the best,
Tom
________________________________
From: Roberto Battistutta
participants (3)
-
Pavel Afonine
-
Roberto Battistutta
-
Tom Burnley - STFC UKRI