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  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
> > 
> > 
> > _______________________________________________
> > phenixbb mailing list
> > [email protected]
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: [email protected]
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Dear Andreas,

I'd rather make the less aware users wonder and ask the more advanced users to 
add the side chains themselves (if the position really does not matter, it is 
easy to script it) than to make the less aware users misinterprete the model.

Best,
Tim


On Friday, February 05, 2016 10:21:05 AM Andreas Forster wrote:
> Tim,
> 
> 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.
> 
> 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.)
> 
> That's why it is critical to model ALL side chains for which there is main
> chain.
> 
> Best
> 
> 
> Andreas
> 
> On Fri, Feb 5, 2016 at 10:13 AM, Tim Gruene  wrote:
> > 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  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
> > > > 
> > > > 
> > > > _______________________________________________
> > > > phenixbb mailing list
> > > > [email protected]
> > > > http://phenix-online.org/mailman/listinfo/phenixbb
> > > > Unsubscribe: [email protected]
> > 
> > --
> > --
> > Paul Scherrer Institut
> > Dr. Tim Gruene
> > - persoenlich -
> > OFLC/102
> > CH-5232 Villigen PSI
> > phone: +41 (0)56 310 5297
> > 
> > GPG Key ID = A46BEE1A
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Pavel, by artefact I mean density which is extremely difficult to interpret. When I worked in the K+ channels, especially the Tl version 1R3J, the difference density looks more pronounced than what I would have expected from ripples alone. As small molecules do not need to follow the symmetry, they tend to be disordered. If this is multiplied by four on a four fold axis, it becomes much harder than anywhere else in the asymmetric unit. I picked up from George Sheldrick that there are artefacts in the FT due to the proximity of special positions. As he usually knows what he is talking about, I trust his opinion, although there is a chance I misunderstood. Maybe you should discuss with him directly (I don't think he reads the phenixbb) for a clarification. Cheers, Tim On Friday, February 05, 2016 07:35:58 AM Pavel Afonine wrote:

Hi,

...

density on symmetry elements usually displays artefacts and is difficult to interpret.

I've seen this rumor perpetuated so many times.. I think I can also say "Fourier maps show artifacts anywhere in the unit cell volume (including symmetry elements) that originate, for example, from: a) finite resolution and partial completeness of the data, b) errors in crystal structure model (model is always used as a source of phase information), c) measurement errors. These artifacts are difficult (and unnecessarily) to interpret in terms of atomic model.". Are symmetry elements somewhat special in this regard (that is one sees more artifacts on symmetry elements than anywhere else)? If this is the case, can someone provide convincing reasoning for this (not hand-waving!)?

Thanks, Pavel

- -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5754 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFWtfqSUxlJ7aRr7hoRAlU9AKCDDnCcInzLD1XxeZ3IfKQVyM8xZwCg626F qYwwnx0FVu4ZrV4frG3GIqE= =2IB2 -----END PGP SIGNATURE-----