<div dir="ltr">Tim,<div><br></div><div>with MD simulation I get the right answer no matter where I model the side chain. As long as it is there, it will be subject to the force field and will move into the right position. If the position is indeed the right one, it will be same no matter where the side chain started out, as long as the simulation reached equilibrium. If the side chain is disordered in the structure, MD will also show that by having the side chain float around aimlessly - but only if it's there in the first place.</div><div><br></div><div>For surface charge plots, I'd argue that the exact position of the charged group doesn't matter either because you don't expect atomic resolution anyway but blue and red patches. However, if the charged residues (which are often flexible) aren't there, you'll just get gray and wonder why the protein is soluble at all. (Actually, you won't. APBS will fail to parametrize the erroneous structure because there are residues with missing atoms.)</div><div><br></div><div>That's why it is critical to model ALL side chains for which there is main chain.</div><div><br></div><div>Best</div><div><br></div><div><br></div><div>Andreas</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 5, 2016 at 10:13 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 Andreas,<br>
<br>
if you use a side chain in an arbitrary orientation, you may get some results<br>
for surface charge plots or molecular dynamics simulation. However, do they<br>
correspond to the experimental data?<br>
<br>
At least when the side chain is missing, it is much easier, especially for<br>
these non-crystallographic applications (or rather crysallographically non-<br>
educated users), to realise they are missing and that appropriate care should<br>
be taken in interpreting the model.<br>
<br>
Your email just underlines how important it is to NOT model side chains when I<br>
don't see density for them: I don't want my models to be misinterpreted, and I<br>
want its users to be made aware of its limits.<br>
<br>
Best,<br>
Tim<br>
<div class="HOEnZb"><div class="h5"><br>
On Friday, February 05, 2016 10:06:10 AM Andreas Forster wrote:<br>
> Dear Jan and Tim,<br>
><br>
> two little comments.<br>
><br>
> If Arg in A clashes with Arg in A* and Arg has multiple conformations,<br>
> couldn't you just fix the occupancy of the clashing conformation to 0.5?<br>
> The two will add up to one, and there won't be a clash left. The remaining<br>
> 0.5 occupancy would be in the other one or more conformations?<br>
><br>
> I agree with Tim regarding artefacts on symmetry axes. However, please<br>
> don't remove side chains that are there. I know this is a contentious<br>
> subject and has been discussed ad nauseam on the CCP4 mailing list, with no<br>
> consensus emerging. To me it is a no-brainer that if a side chain is<br>
> present in the protein, it should be part of the model as well, whether at<br>
> zero occupancy or with mental B values (my preferred way) - though I<br>
> realize that far from everyone finds this argument convincing. However,<br>
> for surface charge plots and for molecular dynamics simulations, complete<br>
> side chains are essential for correct parametrization.<br>
><br>
> All best.<br>
><br>
><br>
> Andreas<br>
><br>
> On Fri, Feb 5, 2016 at 9:35 AM, Tim Gruene <<a href="mailto:tim.gruene@psi.ch">tim.gruene@psi.ch</a>> wrote:<br>
> > Dear Jan,<br>
> ><br>
> > density on symmetry elements usually displays artefacts and is difficult<br>
> > to<br>
> > interpret. If A clashes with A*, this is a real clash and you should not<br>
> > 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>
> ><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<br>
> > > rather<br>
> > > small structure at 2.15Å resolution:<br>
> > ><br>
> > > An Arg side chain is located very close to a crystallographic 2-fold.<br>
> ><br>
> > There<br>
> ><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*,<br>
> > > as<br>
> > > does conformer B. Phenix wants to avoid this 'clash' and moves A and A*<br>
> ><br>
> > out<br>
> ><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>
> ><br>
> > --<br>
> > --<br>
> > Paul Scherrer Institut<br>
> > Dr. Tim Gruene<br>
> > - persoenlich -<br>
> > OFLC/102<br>
> > 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>
> > GPG Key ID = A46BEE1A<br>
> ><br>
> ><br>
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--<br>
--<br>
Paul Scherrer Institut<br>
Dr. Tim Gruene<br>
- persoenlich -<br>
OFLC/102<br>
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>
GPG Key ID = A46BEE1A<br>
<br>
</div></div></blockquote></div><br></div>