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Hi Andrew, you can define a weak bond between clashing atoms which will disable repulsion. A weak bond should not introduce any bias. Pavel On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall < [log in to unmask]> wrote: > Hi all, > > I have a structure of a condensing enzyme with substrate bound. The active > site is very tight, requiring some of the substrate atoms to clash with a > catalytic cysteine. This means that although the substrate fits the density > nicely upon manual real-space refinement, phenix recognises the clash, > resulting in the displacement of substrate atoms so that they are outside > the density. I can mostly fix this by using distance restraints, but I'd > rather allow it to refine in a less biased manner, but ignore the clash. Is > this a acceptable way forward? If so, is there a parameter I can edit to > tell phenix to ignore clashes between these specific atoms? > > Thanks, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > >