Hi Pedro, quick answer: no.
Longer answer: see article "13 typical occupancy refinement scenarios and available options in phenix.refine" here: http://phenix-online.org/newsletter/ Pavel On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias <[email protected]> wrote: > Hi Pavel, > > If the occupancies are 1 does phenix still refine them? Anyway, they can > be explicitly fixed if necessary. > > Pedro > > Às 03:00 de 20/12/2016, Pavel Afonine escreveu: > > Hi Perdo, > > technically this should work too with the caveat that non-blanc altid will > trigger occupancy refinement for corresponding atoms which may not be > desired. > > Pavel > > > On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias <[email protected]> wrote: > >> Hi Andrew, >> >> The simplest way would be to place the "offending" atoms in separate >> conformers as used to refine alternate conformations. This is a 1-letter >> code that goes just before the 3-letter residue name: >> >> ATOM 139 SG *B*CYS A 21 -20.620 4.518 34.501 0.39 >> 12.23 A S >> >> This trick should cause PHENIX to ignore close distances between atoms in >> the A and B conformers. >> >> Hope this helps, >> >> Pedro Matias >> >> >> Às 05:39 de 19/12/2016, Andrew Marshall escreveu: >> >> 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, >> >>
