Hi Andrew, in the past I solved this problem by either switching off certain van der Waals repulsions, or by specifying a very small van der Waals radius for certain atoms. In Xplor/CNX this was rather easy. I do not know how this is with phenix.
Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Andrew Marshall Gesendet: Montag, 19. Dezember 2016 06:39 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Atom clashes in active site? 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
