Tim,

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?

I agree that the 0.98 occupancy should be considered unity, although it might be valid for Julian Chen's crambin structure.

Leif

On Thu, Dec 4, 2014 at 8:46 AM, Tim Gruene <tg@shelx.uni-ac.gwdg.de> wrote:

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Dear Leif,

you can still make use of the X-ray structure if you use external
restraints - they can stabilise the non-H atom structure.

I don't understand why you need free variables for each of the
exchangeable hydrogens. If you were trying to determine the exchange
rate that might be a little over what crystallography can do for you.
Yet, you find a description of how you can do this from occupancy
refinement without the use of an abundant use of free variables in our
paper http://dx.doi.org/10.1107/S1600576713027659
There we made reasonable groups, but if you think you can justify it,
you could do the same for each hydrogen position.

I noticed that there are structures from neutron diffraction in the
PDB with hydrogen occupancies of 0.02 and the respective deuterium at
0.98 - I don't think such an accuracy is justifiable from
crystallographic data, this is merely overfitting the data.

Cheers,
Tim

On 12/04/2014 02:33 PM, Leif Hanson wrote:
> Tim, As I understand joint refinement (although Paul Langan and
> Marat Mustyakimov can give a better answer), the X-ray data are
> used to establish the non-H atom positions, and n0 data to
> establish H and D positions. From a practical standpoint, shelx was
> wonderful for defining the scattering factors of the atoms. But we
> had issues with the length of the input file since we had to create
> free variables for each of the exchangeable hydrogens. With more
> than 400 residues this got a little crazy. Leif
>
> On Thu, Dec 4, 2014 at 4:14 AM, Tim Gruene
> <tg@shelx.uni-ac.gwdg.de> wrote:
>

> Hi Maxime,
>
> you could use shelxl for refinement - it uses the values from the
> Neutron Data Booklet for the most abundant isotopes, and you can
> mix them with your own scattering values without even looking at
> the code. You can even take into account incoherent contributions
> by adjusting the f' and f'' values on the SFAC command like NEUT
> SFAC C H N O S D SFAC FeX 0 0 0 0 0 0 0 0 4.20 0 0 11.220
> 1.23 56 SFAC Co
>
> if you have e.g. Fe-54
>
> If you want to have a joint refinement between X-ray and neutron
> data, I recommend using the X-ray structure by external restraints
> rather than mixing two different types of experiments. You won't
> e.g need to worry about different effective hydrogen bond lengths.
> Published restraints for hydrogen atoms to use with neutron data
> are available from my web-site, for ligands they can be generated
> by the grade-server.
>
> Regards, Tim
>
>
> On 12/03/2014 10:36 PM, Maxime Cuypers wrote:
>>>> Hello,
>>>>
>>>> I would like to alter the neutron scattering table for
>>>> phenix.refine so that it takes into account the correct
>>>> bcoherent value for the metal isotope present in my
>>>> structure. the difference is significative between the
>>>> natural occurence bcoh... i have been looking around in
>>>> chem_data but could not find the neutron scattering tables.
>>>> does anyone have any idea where to look please?
>>>>
>>>> cheerios
>>>>
>>>>
>>>>
>>>> _______________________________________________ phenixbb
>>>> mailing list phenixbb@phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>
>> _______________________________________________ phenixbb mailing
>> list phenixbb@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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