[buster-discuss] Bfactor through bonds

Joshi, Amar (Dr.) aj180 at leicester.ac.uk
Fri Aug 9 16:57:01 CEST 2013


I am refining a protein ligand structure where the core of my ligand is well defined. A terminal aromatic group has electron density for half of the ring while the other portion has poorer density - the ligand is not fully optimised for the pocket.

Buster refinement with the default settings tries to put the whole aromatic group into the strong density. This leads to an increase in clashes and displacement of the core. I would like to reduce the Bfactor through bonds restrains as I want the atoms in weaker elctron density to have greater Bfactor freedom. I have looked in the Appendix 1 but cannot find the appropriate keyword. Is it possible to change this weight? Or do I need to change other weights (eg stereochemistry weight)? And is it possible to change the weights just for the ligand?


Amar Joshi Ph.D

Bayliss Lab
Department of Biochemistry
Henry Wellcome Building
University of Leicester
Lancaster Road, Leicester

Email: aj180 at leicester.ac.uk<mailto:aj180 at leicester.ac.uk>

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