[phenixbb] Dual conformation on symmetry axis

[Tim Gruene]

Dear Andreas,

if you use a side chain in an arbitrary orientation, you may get some results 
for surface charge plots or molecular dynamics simulation. However, do they 
correspond to the experimental data?

At least when the side chain is missing, it is much easier, especially for 
these non-crystallographic applications (or rather crysallographically non-
educated users), to realise they are missing and that appropriate care should 
be taken in interpreting the model.

Your email just underlines how important it is to NOT model side chains when I 
don't see density for them: I don't want my models to be misinterpreted, and I 
want its users to be made aware of its limits.

Best,
Tim

On Friday, February 05, 2016 10:06:10 AM Andreas Forster wrote:
> 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.
> 
> 
> Andreas
> 
> 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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-- 
--
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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