<div dir="ltr">Tim,<div>Let me see if I understand this process flow properly. Let us assume that we have measured two datasets from the same crystal, one neutron, one X-ray (neutron always measured first). I use shelx to refine the x-ray structure to 'stability'. I then use that structure and the input cards from X-ray structure to solve the neutron structure. This is normally what we do. We do not allow the structure to move after X-ray positional refinement, refining only b-factors and occupancies. The primary activity at this point is resolving protonation and water orientation. There are some issues with this strategy (what about X-radiation damage to acidic residues and water molecules?), but it has been reliable to this point. The features for neutron refinement in Phenix as I understand it position the H and D atoms at the end of each major cycle, then complete the b and q refinement. Does this differ from what you are suggesting? </div><div>I agree that the 0.98 occupancy should be considered unity, although it might be valid for Julian Chen's crambin structure. </div><div>Leif</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 4, 2014 at 8:46 AM, Tim Gruene <span dir="ltr"><<a href="mailto:tg@shelx.uni-ac.gwdg.de" target="_blank">tg@shelx.uni-ac.gwdg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">-----BEGIN PGP SIGNED MESSAGE-----<br>
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</span>Dear Leif,<br>
<br>
you can still make use of the X-ray structure if you use external<br>
restraints - they can stabilise the non-H atom structure.<br>
<br>
I don't understand why you need free variables for each of the<br>
exchangeable hydrogens. If you were trying to determine the exchange<br>
rate that might be a little over what crystallography can do for you.<br>
Yet, you find a description of how you can do this from occupancy<br>
refinement without the use of an abundant use of free variables in our<br>
paper <a href="http://dx.doi.org/10.1107/S1600576713027659" target="_blank">http://dx.doi.org/10.1107/S1600576713027659</a><br>
There we made reasonable groups, but if you think you can justify it,<br>
you could do the same for each hydrogen position.<br>
<br>
I noticed that there are structures from neutron diffraction in the<br>
PDB with hydrogen occupancies of 0.02 and the respective deuterium at<br>
0.98 - I don't think such an accuracy is justifiable from<br>
crystallographic data, this is merely overfitting the data.<br>
<br>
Cheers,<br>
Tim<br>
<span class=""><br>
On 12/04/2014 02:33 PM, Leif Hanson wrote:<br>
> Tim, As I understand joint refinement (although Paul Langan and<br>
> Marat Mustyakimov can give a better answer), the X-ray data are<br>
> used to establish the non-H atom positions, and n0 data to<br>
> establish H and D positions. From a practical standpoint, shelx was<br>
> wonderful for defining the scattering factors of the atoms. But we<br>
> had issues with the length of the input file since we had to create<br>
> free variables for each of the exchangeable hydrogens. With more<br>
> than 400 residues this got a little crazy. Leif<br>
><br>
> On Thu, Dec 4, 2014 at 4:14 AM, Tim Gruene<br>
> <<a href="mailto:tg@shelx.uni-ac.gwdg.de">tg@shelx.uni-ac.gwdg.de</a>> wrote:<br>
><br>
</span><div><div class="h5">> Hi Maxime,<br>
><br>
> you could use shelxl for refinement - it uses the values from the<br>
> Neutron Data Booklet for the most abundant isotopes, and you can<br>
> mix them with your own scattering values without even looking at<br>
> the code. You can even take into account incoherent contributions<br>
> by adjusting the f' and f'' values on the SFAC command like NEUT<br>
> SFAC C H N O S D SFAC FeX 0 0 0 0 0 0 0 0 4.20 0 0 11.220<br>
> 1.23 56 SFAC Co<br>
><br>
> if you have e.g. Fe-54<br>
><br>
> If you want to have a joint refinement between X-ray and neutron<br>
> data, I recommend using the X-ray structure by external restraints<br>
> rather than mixing two different types of experiments. You won't<br>
> e.g need to worry about different effective hydrogen bond lengths.<br>
> Published restraints for hydrogen atoms to use with neutron data<br>
> are available from my web-site, for ligands they can be generated<br>
> by the grade-server.<br>
><br>
> Regards, Tim<br>
><br>
><br>
> On 12/03/2014 10:36 PM, Maxime Cuypers wrote:<br>
>>>> Hello,<br>
>>>><br>
>>>> I would like to alter the neutron scattering table for<br>
>>>> phenix.refine so that it takes into account the correct<br>
>>>> bcoherent value for the metal isotope present in my<br>
>>>> structure. the difference is significative between the<br>
>>>> natural occurence bcoh... i have been looking around in<br>
>>>> chem_data but could not find the neutron scattering tables.<br>
>>>> does anyone have any idea where to look please?<br>
>>>><br>
>>>> cheerios<br>
>>>><br>
>>>><br>
>>>><br>
>>>> _______________________________________________ phenixbb<br>
>>>> mailing list <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
>>>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
>>>><br>
><br>
>> _______________________________________________ phenixbb mailing<br>
>> list <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
>><br>
><br>
<br>
- --<br>
- --<br>
Dr Tim Gruene<br>
Institut fuer anorganische Chemie<br>
Tammannstr. 4<br>
D-37077 Goettingen<br>
<br>
GPG Key ID = A46BEE1A<br>
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