5 Feb
2016
5 Feb
'16
8:35 a.m.
Dear Jan, density on symmetry elements usually displays artefacts and is difficult to interpret. If A clashes with A*, this is a real clash and you should not ask for this clash to be ignored. Is this Arg biologically relevant? Otherwise, especially given the medium resolution, you probably create a better model by removing the side chain, even if that leaves difference density. Best, Tim On Thursday, February 04, 2016 01:38:11 PM Jan Abendroth wrote: > Hi all, > I am running into the following problem during the refinement of a rather > small structure at 2.15Å resolution: > > An Arg side chain is located very close to a crystallographic 2-fold. There > is good evidence that the side chain has two conformations. However, > because of the 2-fold, conformer A overlaps with its symmetry mate A*, as > does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out > of the density, same for B and B*. > > Is there a way to avoid this without reducing the symmetry? In the real > crystal, of course the two side chains are agnostic as to if they are > called A or B and will avoid one another ... > > Thanks! > Jan > > -- > Jan Abendroth > Emerald Biostructures > Seattle / Bainbridge Island, WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A