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 <mat...@itqb.unl.pt > <mailto: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 <mailto:mat...@itqb.unl.pt> > > > http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography > > <http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography> > http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit > <http://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 PhD > https://youtu.be/de6j-aaTWNQ > > Master Programme in Biochemistry for Health > https://youtu.be/UKstDCFjYI8 > -- 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-crystallography http://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 PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8
