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Dear Leif,<br>
<br>
thanks for your feedback. The neutron data is to 90% complete. Yes,
you are absolutely right. This is why in the first place I have
refined the structure against neutron data only until convergence.
It's just that we are very much interested in the water structure
and here the addition of the X-ray data helps to orient waters
correctly. The results agree astonishingly well with chemical
intuition which is sometimes not the case when using only neutron
data even though the resolution is comparably high. Waters simply
have too many degrees of freedom and here the knowledge of the
precise oxygen position helps a lot during modelling. Ultimately, we
would like to deposit both, the pure neutron and the XN structure.<br>
<br>
Regards,<br>
Johannes<br>
<p><br>
</p>
<div class="moz-cite-prefix">Am 14.10.2016 um 15:11 schrieb Leif
Hanson:<br>
</div>
<blockquote
cite="mid:CANX_yXKS3nOD5c6WbauzqPF5981kvi8wK3RmCMErx6EBtfq9OA@mail.gmail.com"
type="cite">
<div dir="ltr">Dear Johannes,
<div>What is your completeness in your neutron data? I think at
some point we need to stop hiding behind a joint refinement
and use only the neutron data, especially with this level of
resolution. I like your idea of fixing the ADP ratio. The more
scientifically interesting question in this case is the
exchange and not the B-factors. If you are really bothered by
your X+N H/D coordinate and occupancy results, and your
completeness is near 90% or higher, the more conservative
result is to refine with SHELX.</div>
<div>Best wishes,</div>
<div>Leif Hanson</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Oct 14, 2016 at 5:45 AM,
Johannes Schiebel <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:johannes.schiebel2@gmail.com" target="_blank">johannes.schiebel2@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Dear Tim,<br>
<br>
thank you very much for your reply! I agree that it will
be very difficult to get reasonable values for both,
occupancy and ADPs, at usual neutron diffraction
resolutions of around 2 A. However, we are talking about
neutron diffraction data to 1.4 A and X-ray diffraction
data to 0.9 A. So, we have a lot of data. I should have
mentioned this right away, sorry. Do you think that in
such a rare case it might be possible to get reasonable
values?<br>
<br>
Also, I like your idea to group H/D sites by expected
exchange values. However, from the high-quality data we
have, it is obvious that in a lot of cases the exchange
rate is not really easy to predict by chemical intuition
alone. There are sites where you clearly would expect at
least a partial exchange but yet you observe a strong
negative peak in the neutron scattering length density
indicating the presence of an almost non-exchanged
hydrogen . Wouldn't it also be possible to fix the ADP
ratio between the H/D atoms and the atom to which they are
attached to a chemically likely value between 1.0 and 1.5
and then refine only the occupancy? To me auch an approach
seems less prone to errors introduced into the model by
the crystallographer's expectations.<br>
<br>
Best wishes,<br>
Johannes
<div>
<div class="h5"><br>
<br>
<br>
<div class="m_-7779928436125602962moz-cite-prefix">Am
13.10.2016 um 17:25 schrieb Tim Gruene:<br>
</div>
<blockquote type="cite">
<pre>Dear Johannes,
I would recommend not to refine the occupancy of individual H/D pairs, unless
you have high resolution and other evidence for the resulting values.
Occupancy and ADP-values are very strongly correlated, and the correlation
becomes higher the worse your resolution. And neutron data often have
resolution of 2A or worse.
You could group atoms together where you expect similar exchange ratios (based
on chemical intuition) and refine one ratio per group. You can find a more
detailed explanation in <a moz-do-not-send="true" class="m_-7779928436125602962moz-txt-link-freetext" href="https://doi.org/10.1107/S1600576713027659" target="_blank">https://doi.org/10.1107/<wbr>S1600576713027659</a>
That article also recommends to treat X-ray data as additional information by
means of geometry restraints to avoid the complications you get with joint
refinement. The main effect of joint refinement are prettier maps <flame> and
you may need to decide whether you want to focus on science or on art
</flame>. This way we refined the structure also has the side effect to
constrain H and D to the same location, although, admittedly, the coordinate
difference in the structure you quote is probably negligible.
Best,
Tim
On Thursday, October 13, 2016 05:06:36 PM Johannes Schiebel wrote:
</pre>
<blockquote type="cite">
<pre>Hi everyone,
I am currently working on an X-ray/neutron (XN) joint refinement using
phenix.refine. As it should be, H/D coordinates and ADPs at exchangable
sites are refined to equal values when using Phenix version 1.10.1-2155
and neutron data only. This is also stated in the paper describing the
development of the method (Afonine et al. (2010) Joint X-ray and neutron
refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66,
1153-1163) as the default behavior: "Currently, phenix.refine maintains
the H and D atoms at coinciding positions and constrains their ADPs to
be equal to each other". However, when switching to XN-refinement using
the same Phenix version, H and D atoms refine to different coordinates
and ADPs, which should not be the case as it leads to unrealistic
artifacts as can be seen from the deposited PDB 3X2P:
ATOM 186 H AALA A 13 3.486 -18.200 -14.123 0.38
14.54 H
ATOM 187 D BALA A 13 3.488 -18.195 -14.111 0.62
38.07 D
In this example, the D-occupancy is likely overestimated, while the
H-occupancy is underestimated because the ADPs refine to very different
values, which is chemically not reasonable.
Hence my question: How can I treat my data in a way that ADPs and
coordinates refine to the same values at exchangeable H/D sites also for
XN-refinement? Is there a specific keyword I am currently overlooking or
do I have to use another Phenix version?
I would be really glad to receive your feedback. Thanks in advance!
Kind regards,
Johannes
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