[phenixbb] Dual conformation on symmetry axis

Andreas Forster docandreas at gmail.com
Fri Feb 5 01:06:10 PST 2016

Dear Jan and Tim,

two little comments.

If Arg in A clashes with Arg in A* and Arg has multiple conformations,
couldn't you just fix the occupancy of the clashing conformation to 0.5?
The two will add up to one, and there won't be a clash left.  The remaining
0.5 occupancy would be in the other one or more conformations?

I agree with Tim regarding artefacts on symmetry axes.  However, please
don't remove side chains that are there.  I know this is a contentious
subject and has been discussed ad nauseam on the CCP4 mailing list, with no
consensus emerging.  To me it is a no-brainer that if a side chain is
present in the protein, it should be part of the model as well, whether at
zero occupancy or with mental B values (my preferred way) - though I
realize that far from everyone finds this argument convincing.  However,
for surface charge plots and for molecular dynamics simulations, complete
side chains are essential for correct parametrization.

All best.


On Fri, Feb 5, 2016 at 9:35 AM, Tim Gruene <tim.gruene at psi.ch> wrote:

> 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
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