Hi Andrew, yes, exactly as you describe: set distance_ideal to a meaningful value (approx. distance between density peaks, doesn't have to be very accurate), and set sigma to some large number, say 1 or so.
Pavel On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall < [email protected]> wrote: > Hi Pavel, > > To define a weak bond, would you use "geometry_restraints.edits { ... bond > {... " , and just set a rough distance_ideal and a very high sigma (like > say 5A)? > Or are you referring to something different? > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine <[email protected]> wrote: > >> 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 < >> [email protected]> 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 >>> >>> >> >
