[phenixbb] how to inhibit selectively undue H....O repulsion during refinement with phenix.refine ?

Pavel Afonine pafonine at lbl.gov
Sat Feb 10 10:48:33 PST 2018

Hi Maxime,

> i am refining neutron data with hydrogens on water molecules complexes 
> that systematically bounce the whole molecule away from the hydroxyls 
> or carboxylic groups or other waters. the Fo-Fc map is crystal clear 
> about where the H atoms should go...
> any commands i can enter in i.e. a .param file to inhibit repulsion 
> and promote closer h bonds?
> thanks for your help,

I can investigate this and see what can be done. For this could you 
please send me an example? I'll need PDB files before and after 
refinement, reflection data file, any ligand cif files if used and 
indicate atoms in question..


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