[phenixbb] Switching off symmetry related van der waals in phenix.refine

Chandrika Deshpande cdeshpan at cbms.mq.edu.au
Thu Apr 30 19:33:08 PDT 2009

Hello everyone,

I am using Phenix.refine to refine one of my protein structures.

My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes a problem which I need to solve :

How can I refine this structure to include the PEG molecule?

Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ?

Is there a way to switch off symmetry related van der waals terms from the penalty function in phenix.refine ?

I have already tried refining by changing the occupancy of PEG to 0.5 but this does not work as after running refinement the PEG molecule is pushed out of the electron density map.


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