<div dir="ltr">Dear Jan and Tim,<div><br></div><div>two little comments.</div><div><br></div><div>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?</div><div><br></div><div>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.</div><div><br></div><div>All best.</div><div><br></div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 5, 2016 at 9:35 AM, Tim Gruene <span dir="ltr"><<a href="mailto:tim.gruene@psi.ch" target="_blank">tim.gruene@psi.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Jan,<br>
<br>
density on symmetry elements usually displays artefacts and is difficult to<br>
interpret. If A clashes with A*, this is a real clash and you should not ask<br>
for this clash to be ignored.<br>
<br>
Is this Arg biologically relevant? Otherwise, especially given the medium<br>
resolution, you probably create a better model by removing the side chain,<br>
even if that leaves difference density.<br>
<br>
Best,<br>
Tim<br>
<div class="HOEnZb"><div class="h5"><br>
On Thursday, February 04, 2016 01:38:11 PM Jan Abendroth wrote:<br>
> Hi all,<br>
> I am running into the following problem during the refinement of a rather<br>
> small structure at 2.15Å resolution:<br>
><br>
> An Arg side chain is located very close to a crystallographic 2-fold. There<br>
> is good evidence that the side chain has two conformations. However,<br>
> because of the 2-fold, conformer A overlaps with its symmetry mate A*, as<br>
> does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out<br>
> of the density, same for B and B*.<br>
><br>
> Is there a way to avoid this without reducing the symmetry? In the real<br>
> crystal, of course the two side chains are agnostic as to if they are<br>
> called A or B and will avoid one another ...<br>
><br>
> Thanks!<br>
> Jan<br>
><br>
> --<br>
> Jan Abendroth<br>
> Emerald Biostructures<br>
> Seattle / Bainbridge Island, WA, USA<br>
> home: <a href="http://Jan.Abendroth_at_gmail.com" rel="noreferrer" target="_blank">Jan.Abendroth_at_gmail.com</a><br>
> work: JAbendroth_at_embios.com<br>
> <a href="http://www.emeraldbiostructures.com" rel="noreferrer" target="_blank">http://www.emeraldbiostructures.com</a><br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
--<br>
Paul Scherrer Institut<br>
Dr. Tim Gruene<br>
- persoenlich -<br>
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CH-5232 Villigen PSI<br>
phone: <a href="tel:%2B41%20%280%2956%20310%205297" value="+41563105297">+41 (0)56 310 5297</a><br>
<br>
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