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 <mat...@itqb.unl.pt> 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, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > > -- > > Industry and Medicine Applied Crystallography > Macromolecular Crystallography Unit > ___________________________________ > Phones : (351-21) 446-9100 Ext. 1669 > (351-21) 446-9669 (direct) > Fax : (351-21) 441-1277 or 443-3644 > > email : mat...@itqb.unl.pt > http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallographyhttp://www.itqb.unl.pt/labs/macromolecular-crystallography-unit > > Mailing address : > Instituto de Tecnologia Quimica e Biologica António Xavier > Universidade Nova de Lisboa > Av. da República > 2780-157 Oeiras > PORTUGAL > > ITQB NOVA, a great choice for your PhDhttps://youtu.be/de6j-aaTWNQ > > Master Programme in Biochemistry for Healthhttps://youtu.be/UKstDCFjYI8 > >
