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October 2026

4 participants
2 discussions

DEN restraints and ECHT disorder models
by Roberto Battistutta 19 Oct '26

19 Oct '26

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 roberto.battistutta(a)unipd.it

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B-factors increase for ligands, phenix 2.2.1-6174
by jan.abendroth＠ucb.com 03 Oct '26

03 Oct '26

Hi all, I have seen this odd behavior with a couple of ligands in phenix 2.2.1-6174: B-factors of some well-defined ligands increase significantly during a refinement, in the range of 2-fold compared with surrounding protein residues. The density hints for full occupancy - just about as strong as for the neighboring residues. As a test, I changed the occupancy of the ligand to 0.8. Phenix refines back to 1.0. If I turn off occupancy refinement, B-factors for the ligand increase even more. While the geometry looks fine, I am left with significant positive difference density. I have refined several structures for both targets with different ligands and never ran into this. Has this been seen before and is there anything I could try? I have already tested versions 6190 and 6048 and see the same behavior. Thanks, Jan

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